VMD-L Mailing List

From: Dr. Daniel James White PhD (dan_at_chalkie.org.uk)
Date: Thu Jun 12 2003 - 08:51:23 CDT

Hi all,

I wish to perform interactive molecular dynamics, actually interactive
energy minimisation
using namd2 with VMD

I have made the pdb and psf files for the large protein model (110
residues)
using psfgen and an amber parameter and topology files I found on the
internet named:
par_all27_prot_na.inp
and
top_all27_prot_na.inp
which seem to contain all the parameters adn topologies for the 22
amino acids and also nucleic acids and some metals etc.

1) Are these 2 files listed above the right files to use? If not, where
should I find the most recent up to date ones?
2) Why does psfgen make the hydrogens on my proline residues in rather
horrible looking places?
3) Can someone suggest a sensible namd2 .conf file for doing an
interactive energy minimisation on this large molecular model?
4) What does NaN mean in my namd2 terminal output?

below is my current .conf file
running namd 2 wit this results in parts of the protein vanishing from
the VMD graphics window until there is nothing left.
the terminal output is below also

cheers

Dan

# This is a namd configuration file for interactive minimisation of
proteins

#integrator
timestep 1.0
#numsteps 100000

#molecular system
structure output/a2allfrompsfgen.psf
coordinates output/a2allfrompsfgen.pdb

#force field
parameters par_all27_prot_na.inp
paraTypeCharmm on
exclude scaled1-4
1-4scaling 1

#output
outputname output/a2allafternamd.pdb
#dcdfrequency 1000
#outputenergies 10
#outputtiming 100
binaryoutput no

#approximations
margin 0
stepspercycle 20
switching on
switchdist 5
cutoff 8
pairlistdist 13.5

#Protocol
temperature 0
reassignFreq 1000
reassignTemp 25
reassignIncr 25
reassignHold 300

#langevin on
#langevinDamping 1
#langevinHydrogen no
#langevinTemp 300
#minimization on

#IMD
IMDon yes
IMDport 2030
IMDfreq 1
IMDwait on

#script
minimize 1000
run 20000

[daniel:stuff/modelling/namd_modelling] dan% namd2
interactive_minimisation.conf
Charm++: standalone mode (not using charmrun)
Charm++: scheduler running in netpoll mode.
Info: NAMD 2.5b1 for Darwin-PPC
Info:
Info: Please visit http://www.ks.uiuc.edu/Research/namd/
Info: and send feedback or bug reports to namd_at_ks.uiuc.edu
Info:
Info: Please cite Kale et al., J. Comp. Phys. 151:283-312 (1999)
Info: in all publications reporting results obtained with NAMD.
Info:
Info: Sending usage information to NAMD developers via UDP.
Info: Sent data is: 1 NAMD 2.5b1 Darwin-PPC 1 daniel.bio.jyu.fi
dan
Info: Running on 1 processors.
Info: 0 kB of memory in use.
Measuring processor speeds... Done.
Info: Configuration file is interactive_minimisation.conf
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: MAX SELF PARTITIONS 50
Info: MAX PAIR PARTITIONS 20
Info: SELF PARTITION ATOMS 125
Info: PAIR PARTITION ATOMS 200
Info: PAIR2 PARTITION ATOMS 400
Info: INITIAL TEMPERATURE 0
Info: CENTER OF MASS MOVING? NO
Info: DIELECTRIC 1
Info: EXCLUDE SCALED ONE-FOUR
Info: 1-4 SCALE FACTOR 1
Info: NO DCD TRAJECTORY OUTPUT
Info: NO EXTENDED SYSTEM TRAJECTORY OUTPUT
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME output/a2allafternamd.pdb
Info: NO RESTART FILE
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8
Info: SWITCHING OFF 12
Info: PAIRLIST DISTANCE 13.5
Info: MARGIN 0
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 16
Info: INTERACTIVE MD ACTIVE
Info: INTERACTIVE MD PORT 2030
Info: INTERACTIVE MD FREQ 1
Info: WILL AWAIT INTERACTIVE MD CONNECTION
Info: VELOCITY REASSIGNMENT FREQ 1000
Info: VELOCITY REASSIGNMENT TEMP 25
Info: VELOCITY REASSIGNMENT INCR 25
Info: VELOCITY REASSIGNMENT HOLD 300
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: RANDOM NUMBER SEED 1055425634
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB output/a2allfrompsfgen.pdb
Info: STRUCTURE FILE output/a2allfrompsfgen.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_na.inp

Warning: DUPLICATE DIHEDRAL ENTRY FOR CP1-C-N-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CP3-N-C-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-N-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-N-CP3
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-C-NH1-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-CT2-CPH1-CPH1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.27 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-CT2-CPH1-CPH1
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.2 n=1 delta=0
   k=0.27 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT1-NH1-C-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-N-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-N-CP3
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT2
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-C-NH1-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-NH1-C-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-NH1-C-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-SM-SM-CT2
PREVIOUS VALUES MULTIPLICITY: 1
   k=1 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=4.1 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT2-SM-SM-CT2
PREVIOUS VALUES MULTIPLICITY: 2
   k=1 n=1 delta=0
   k=4.1 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.9 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-N-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-N-CP3
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT2
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-C-NH1-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-CPH1-CPH1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.27 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-CPH1-CPH1
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.2 n=1 delta=0
   k=0.27 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-CT2-S-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.24 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.37 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-NH1-C-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-NH1-C-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.6 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=2.5 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-S-CT2-CT2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.24 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.37 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-SM-SM-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=1 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=4.1 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CT3-SM-SM-CT3
PREVIOUS VALUES MULTIPLICITY: 2
   k=1 n=1 delta=0
   k=4.1 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.9 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.33 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.18 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT1
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.33 n=1 delta=0
   k=0.18 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.32 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.33 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.18 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT1-CT3
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.33 n=1 delta=0
   k=0.18 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.32 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.3 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT1
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.3 n=1 delta=0
   k=0.3 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.42 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT2
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.3 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT2
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.3 n=1 delta=0
   k=0.3 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.42 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.3 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR H-OH1-CT2-CT3
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.3 n=1 delta=0
   k=0.3 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.42 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.24 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.15 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT1
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.24 n=1 delta=0
   k=0.15 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.27 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.24 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.15 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR HS-S-CT2-CT3
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.24 n=1 delta=0
   k=0.15 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.27 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-CP2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-HB
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR N-C-CP1-N
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.3 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=-0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-CP2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-HB
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR NH1-C-CP1-N
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.3 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=-0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-CP2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-HB
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR NH2-CC-CP1-N
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.3 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=-0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-CP1-CP2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-CP1-HB
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-N-CP1
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR O-C-N-CP3
PREVIOUS VALUES MULTIPLICITY: 1
   k=2.75 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR O-CC-CP1-CP2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR O-CC-CP1-HB
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.6 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR OB-CD-OS-CT2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.965 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=3.85 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR OB-CD-OS-CT3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.965 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=3.85 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CA-CA-ON2b-P
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.4 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CA-ON2b-P-ON4
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.95 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN7
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.2 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.1 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN7
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.1 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN7
PREVIOUS VALUES MULTIPLICITY: 3
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
   k=0.1 n=3 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0 n=6 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN8
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.2 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.1 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN8
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.1 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN8
PREVIOUS VALUES MULTIPLICITY: 3
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
   k=0.1 n=3 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0 n=6 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN8B
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.2 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.1 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN8B
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.1 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN8B
PREVIOUS VALUES MULTIPLICITY: 3
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
   k=0.1 n=3 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0 n=6 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN9
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.2 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.1 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN9
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.1 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-P-ON2-CN9
PREVIOUS VALUES MULTIPLICITY: 3
   k=1.2 n=1 delta=180
   k=0.1 n=2 delta=180
   k=0.1 n=3 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0 n=6 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON4-P-ON2-CN7
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.95 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON4-P-ON2-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.95 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON4-P-ON2-CN8
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.95 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON4-P-ON2-CN8B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.95 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON4-P-ON2-CN9
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.95 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN3A-CN3-CN1A-NN1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.35 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.62 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN3B-CN3-CN1A-NN1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.35 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.62 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN3-CN1A-ON1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=1 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN3-CN1A-ON1
PREVIOUS VALUES MULTIPLICITY: 2
   k=1 n=2 delta=180
   k=1 n=3 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.4 n=6 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN3-CN1A-NN1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.5 n=2 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.35 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN3-CN1A-NN1
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.5 n=2 delta=180
   k=0.35 n=3 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.4 n=6 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN3C-CN3-CN1A-ON1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.3 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=1.95 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN3C-CN3-CN1A-NN1
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.1 n=1 delta=180
INCREASING MULTIPLICITY TO: 2
   k=1.95 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR P2-ON2-P-ON2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.03 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR P-ON2-P2-ON2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.03 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR P2-ON2-P2-ON2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.03 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR P-ON2-P-ON2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.03 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR P-ON2-P-ON3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.1 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR P-ON2-P2-ON3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.1 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR P2-ON2-P-ON3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.1 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR P2-ON2-P2-ON3
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.1 n=2 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.03 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-CN7
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.4 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-CN7
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.8 n=6 delta=0
   k=0.4 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7B-CN7-CN7
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.4 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7B-CN7-CN7
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.8 n=6 delta=0
   k=0.4 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-CN7
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.4 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-CN7
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.8 n=6 delta=0
   k=0.4 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7B-ON6
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.5 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7B-ON6
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.5 n=6 delta=0
   k=0.3 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.6 n=4 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7B-ON6
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.5 n=6 delta=0
   k=0.3 n=5 delta=0
   k=0.6 n=4 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0.2 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6-CN7B-NR1-CPH1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=2 delta=-70

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6-CN7B-NR1-CPH1
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.2 n=3 delta=0
   k=0.5 n=2 delta=-70
INCREASING MULTIPLICITY TO: 3
   k=0.6 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6B-CN7B-NR1-CPH1
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=2 delta=-70

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6B-CN7B-NR1-CPH1
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.2 n=3 delta=0
   k=0.5 n=2 delta=-70
INCREASING MULTIPLICITY TO: 3
   k=0.6 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN7B-NR1-CPH2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.1 n=3 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN7B-NR1-CPH2
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.1 n=3 delta=180
   k=0.3 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7B-CN7B-NR1-CPH2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.1 n=3 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7B-CN7B-NR1-CPH2
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.1 n=3 delta=180
   k=0.3 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6-CN7B-NN2B-CN1T
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.7 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.8 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6B-CN7B-NN2B-CN1T
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.7 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.8 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6-CN7B-NN2B-CN5
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=1.1 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON6B-CN7B-NN2B-CN5
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=1.1 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN8B-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 1
   k=1.33 n=1 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.18 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN8B-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 2
   k=1.33 n=1 delta=0
   k=0.18 n=2 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.32 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-CN8B-ON2
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=4 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.8 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-CN8B-ON2
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.2 n=4 delta=180
   k=0.8 n=3 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.4 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-CN8B-ON2
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.2 n=4 delta=180
   k=0.8 n=3 delta=180
   k=0.4 n=2 delta=0
INCREASING MULTIPLICITY TO: 4
   k=2.5 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-CN8B-ON5
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=4 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.8 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-CN8B-ON5
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.2 n=4 delta=180
   k=0.8 n=3 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.4 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-CN8B-ON5
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.2 n=4 delta=180
   k=0.8 n=3 delta=180
   k=0.4 n=2 delta=0
INCREASING MULTIPLICITY TO: 4
   k=2.5 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-CN8B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=4 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.8 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-CN8B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.2 n=4 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.8 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-ON6
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.5 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-ON6
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.5 n=6 delta=0
   k=0.3 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.6 n=4 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-ON6
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.5 n=6 delta=0
   k=0.3 n=5 delta=0
   k=0.6 n=4 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0.2 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-ON6B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-ON6B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.4 n=6 delta=0
   k=0 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=4 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7-ON6B
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.4 n=6 delta=0
   k=0 n=5 delta=0
   k=0 n=4 delta=180
INCREASING MULTIPLICITY TO: 4
   k=1.6 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7B-CN7B-ON6B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7B-CN7B-ON6B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.4 n=6 delta=0
   k=0 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=4 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7B-CN7B-ON6B
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.4 n=6 delta=0
   k=0 n=5 delta=0
   k=0 n=4 delta=180
INCREASING MULTIPLICITY TO: 4
   k=1.6 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-ON6
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.5 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-ON6
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.5 n=6 delta=0
   k=0.3 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0.6 n=4 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-ON6
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.5 n=6 delta=0
   k=0.3 n=5 delta=0
   k=0.6 n=4 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0.2 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-ON6B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.4 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-ON6B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.4 n=6 delta=0
   k=0 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=4 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7-ON6B
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.4 n=6 delta=0
   k=0 n=5 delta=0
   k=0 n=4 delta=180
INCREASING MULTIPLICITY TO: 4
   k=1.6 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN8-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.4 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN8-CN7B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.8 n=6 delta=0
   k=0.4 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7B-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.6 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7B-CN7B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.6 n=6 delta=0
   k=0 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=1.6 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7C-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.4 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON2-CN7-CN7C-CN7B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.8 n=6 delta=0
   k=0.4 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN8-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.4 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN8-CN7B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.8 n=6 delta=0
   k=0.4 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7B-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.6 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7B-CN7B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.6 n=6 delta=0
   k=0 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=1.6 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7C-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=6 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.4 n=5 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR ON5-CN7-CN7C-CN7B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.8 n=6 delta=0
   k=0.4 n=5 delta=0
INCREASING MULTIPLICITY TO: 3
   k=2 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-ON2-P
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.6 n=5 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.2 n=4 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-ON2-P
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.6 n=5 delta=0
   k=0.2 n=4 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=3 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-ON2-P
PREVIOUS VALUES MULTIPLICITY: 3
   k=0.6 n=5 delta=0
   k=0.2 n=4 delta=0
   k=0 n=3 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0.4 n=2 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-ON2-P
PREVIOUS VALUES MULTIPLICITY: 4
   k=0.6 n=5 delta=0
   k=0.2 n=4 delta=0
   k=0 n=3 delta=180
   k=0.4 n=2 delta=0
INCREASING MULTIPLICITY TO: 5
   k=1.9 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.5 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.3 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7-CN7-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.5 n=3 delta=0
   k=0.3 n=2 delta=180
INCREASING MULTIPLICITY TO: 3
   k=1.5 n=1 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN7-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.5 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=1 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN8-CN7-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 2
   k=0.5 n=3 delta=0
   k=1 n=2 delta=180
INCREASING MULTIPLICITY TO: 3
   k=0.3 n=1 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7B-CN7-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=1 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR CN7C-CN7-ON5-HN5
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.8 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0.5 n=1 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR HN5-ON5-CN7B-CN7B
PREVIOUS VALUES MULTIPLICITY: 1
   k=0 n=6 delta=180
INCREASING MULTIPLICITY TO: 2
   k=0.8 n=3 delta=0

Warning: DUPLICATE DIHEDRAL ENTRY FOR HN5-ON5-CN7B-CN7B
PREVIOUS VALUES MULTIPLICITY: 2
   k=0 n=6 delta=180
   k=0.8 n=3 delta=0
INCREASING MULTIPLICITY TO: 3
   k=0 n=2 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR HN5-ON5-CN7B-CN7B
PREVIOUS VALUES MULTIPLICITY: 3
   k=0 n=6 delta=180
   k=0.8 n=3 delta=0
   k=0 n=2 delta=180
INCREASING MULTIPLICITY TO: 4
   k=0 n=1 delta=180

Warning: DUPLICATE DIHEDRAL ENTRY FOR HN5-ON5-CN7B-CN7
PREVIOUS VALUES MULTIPLICITY: 1
   k=0.3 n=3 delta=0
INCREASING MULTIPLICITY TO: 2
   k=0 n=1 delta=0
Info: SUMMARY OF PARAMETERS:
Info: 250 BONDS
Info: 622 ANGLES
Info: 1049 DIHEDRAL
Info: 73 IMPROPER
Info: 130 VDW
Info: 0 VDW_PAIRS
Info: ****************************
Info: STRUCTURE SUMMARY:
Info: 17237 ATOMS
Info: 17408 BONDS
Info: 31420 ANGLES
Info: 46034 DIHEDRALS
Info: 3040 IMPROPERS
Info: 0 EXCLUSIONS
Info: 51708 DEGREES OF FREEDOM
Info: 8690 HYDROGEN GROUPS
Info: TOTAL MASS = 123513 amu
Info: TOTAL CHARGE = -26.18 e
Info: *****************************
Info: Entering startup phase 0 with 0 kB of memory in use.
Info: Entering startup phase 1 with 0 kB of memory in use.
Info: Entering startup phase 2 with 0 kB of memory in use.
Info: Entering startup phase 3 with 0 kB of memory in use.
Info: PATCH GRID IS 4 BY 15 BY 5
Info: REMOVING COM VELOCITY 0 0 0
Info: Entering startup phase 4 with 0 kB of memory in use.
Info: Entering startup phase 5 with 0 kB of memory in use.
Info: Entering startup phase 6 with 0 kB of memory in use.
Info: Entering startup phase 7 with 0 kB of memory in use.
Info: COULOMB TABLE R-SQUARED SPACING: 0.0625
Info: COULOMB TABLE SIZE: 2309 POINTS
Info: NONZERO IMPRECISION IN COULOMB TABLE: 3.30872e-24 0
Info: Entering startup phase 8 with 0 kB of memory in use.
Info: Finished startup with 0 kB of memory in use.
TCL: Minimizing for 1000 steps
Info: INTERACTIVE MD AWAITING CONNECTION
ETITLE: TS BOND ANGLE DIHED IMPRP ELECT
       VDW BOUNDARY MISC KINETIC TOTAL TEMP
ENERGY: 0 3085.2929 NaN NaN 1525.3415
-16673.5193 28542.4820 0.0000 0.0000 0.0000 NaN
0.0000
INITIAL STEP: 1e-06
GRADIENT TOLERANCE: NaN
ENERGY: 1 NaN NaN NaN NaN NaN
    NaN 0.0000 0.0000 0.0000 NaN 0.0000
BRACKET: NaN NaN NaN NaN NaN
RESTARTING CONJUGATE GRADIENT ALGORITHM
INITIAL STEP: 2.5e-07
GRADIENT TOLERANCE: NaN
^C

Dr. Daniel James White BSc. (Hons.) PhD
Cell Biology
Department of biological and environmental science
PO Box 35
University of Jyväskylä
Jyväskylä FIN 40014
Finland
+358 (0)14 260 4183 (work)
+358 (0)414740463 (mob)

http://www.chalkie.org.uk
dan_at_chalkie.org.uk
white_at_cc.jyu.fi