Re: usage of NAMD with AMBER commands

From: francesco oteri (francesco.oteri_at_gmail.com)
Date: Tue Jun 15 2010 - 16:29:15 CDT

The problem is that 2.7b2 has a bug regarding AMBER force field.
Since a guy solved the problem, check the mailing list to find the patch to
apply to solve this problem.
Alternatively, you can use the nightly builded version, but I don't know if
the last version of namd has been generated with this patch.

2010/6/15 Thomas C. Bishop <bishop_at_tulane.edu>

> It looks like NAMD properly reads the amber parm/top files so assuming NAMD
> actually runs (you did run an example system already right?) it seems you
> may
> have done something wrong w/ the build up of the system in tleap.
>
> Does the structure summary for the amber.parm/top seem right? Can you load
> it
> in VMD ? (note if it's amber parm7 or older parm format)
>
> Have you built up the molec w/ charm topology to compare w/ AMBER?
> This is useful exercise to make sure you are really setting all inputs
> properly (like the scee factor)
>
> My guess is your periodic box is wrong OR you have bad coordinate info. By
> bad
> coord info I mean either NAMD is misreading some coordinate information so
> the
> energy/force calcs die or there are some nasty clashes in your system and
> NAMD
> is reading them correctly... it's just a bad structure.
>
> Taking a look w/ VMD should help you in either case.
> If you can get just 1 energy calc then it's very very likely a system
> build/setup problem not a namd problem but w/out even one energy calc seems
> like it could be a NAMD problem.
>
> keep me/use posted. I 'd like to hear what you find.
>
> Tom
>
>
> On Tuesday 15 June 2010 11:51:08 am Giovanni Nico wrote:
> > Dear NAMD users,
> >
> > I just started using NAMD. I installed the version 2.7b2 on a
> > 64 bit machine (ubutu operative system).
> >
> > I successfully ran a configuration file taken from tutorial files. Then,
> > to learn more about
> > the use of the AMBER field I replaced the commands
> >
> > > coordinates <..>.pdb
> > > structure <..>.psf
> > > parameters par_all27_prot_lipid_na.inp
> > > paratypecharmm on
> >
> > with the following ones
> >
> > > amber yes
> > > parmfile <...>.prmtop #AMBER topology
> > > ambercoor <...>.prmcrd #coordinates
> >
> > I created prmtop and coordinate files via
> >
> > > XLEAP from AmberTools. I used the following commands
> > >
> > > source leaprc.ff99SB
> > > loadPdb heating_example.pdb
> > > saveAmberParm x prmtop prmcrd
> >
> > Unfortunately, I got a SEGMENTATION FAULT message (see text after the
> > CUT HERE at the end of this message!)
> >
> > Did I some mistakes when installing NAMD?
> > Is this related to the NAMD version (2.7b2 on a 64 bit machine?)
> > Did I need to properly set a parameter to use AMBER?
> > Is this related to the usage of AMBER commands?
> > Is there any other possible explanation?
> >
> > Thank you for your help!
> >
> > regards,
> > giovanni
> >
> > ================================ CUT HERE
> > ====================================
> >
> > Charm++: standalone mode (not using charmrun)
> > Charm++> cpu topology info is being gathered.
> > Charm++> Running on 1 unique compute nodes (4-way SMP).
> > Info: NAMD 2.7b2 for Linux-x86_64
> > 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 Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)
> > Info: in all publications reporting results obtained with NAMD.
> > Info:
> > Info: Based on Charm++/Converse 60103 for net-linux-x86_64-iccstatic
> > Info: Built Thu Nov 12 22:12:21 CST 2009 by jim on belfast.ks.uiuc.edu
> > Info: 1 NAMD 2.7b2 Linux-x86_64 1 quad2-desktop rocco
> > Info: Running on 1 processors.
> > Info: CPU topology information available.
> > Info: Charm++/Converse parallel runtime startup completed at 0.00371122 s
> > Info: 1.50945 MB of memory in use based on CmiMemoryUsage
> > Info: Configuration file is min.conf
> > TCL: Suspending until startup complete.
> > Warning: The following variables were set in the
> > Warning: configuation file but were not needed
> > Warning: switchdist
> > Info: SIMULATION PARAMETERS:
> > Info: TIMESTEP 2
> > Info: NUMBER OF STEPS 2000
> > Info: STEPS PER CYCLE 10
> > Info: PERIODIC CELL BASIS 1 83.04 0 0
> > Info: PERIODIC CELL BASIS 2 0 70.67 0
> > Info: PERIODIC CELL BASIS 3 0 0 60.45
> > Info: PERIODIC CELL CENTER 43.2187 36.528 31.4622
> > Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
> > Info: LOAD BALANCE STRATEGY New Load Balancers -- ASB
> > Info: LDB PERIOD 2000 steps
> > Info: FIRST LDB TIMESTEP 50
> > Info: LAST LDB TIMESTEP -1
> > Info: LDB BACKGROUND SCALING 1
> > Info: HOM BACKGROUND SCALING 1
> > Info: PME BACKGROUND SCALING 1
> > Info: MAX SELF PARTITIONS 20
> > Info: MAX PAIR PARTITIONS 8
> > Info: SELF PARTITION ATOMS 154
> > Info: SELF2 PARTITION ATOMS 154
> > Info: PAIR PARTITION ATOMS 318
> > Info: PAIR2 PARTITION ATOMS 637
> > Info: MIN ATOMS PER PATCH 100
> > Info: INITIAL TEMPERATURE 0
> > Info: CENTER OF MASS MOVING INITIALLY? NO
> > Info: DIELECTRIC 1
> > Info: EXCLUDE SCALED ONE-FOUR
> > Info: 1-4 SCALE FACTOR 0.83333
> > Info: DCD FILENAME outputs/1hjn3_min.coor.dcd
> > Info: DCD FREQUENCY 2000
> > Info: DCD FIRST STEP 2000
> > Info: DCD FILE WILL CONTAIN UNIT CELL DATA
> > Info: XST FILENAME outputs/1hjn3_min.xst
> > Info: XST FREQUENCY 2000
> > Info: VELOCITY DCD FILENAME outputs/1hjn3_min.vel.dcd
> > Info: VELOCITY DCD FREQUENCY 2000
> > Info: VELOCITY DCD FIRST STEP 2000
> > Info: OUTPUT FILENAME outputs/1hjn3_min
> > Info: BINARY OUTPUT FILES WILL BE USED
> > Info: RESTART FILENAME outputs/1hjn3_min.rst
> > Info: RESTART FREQUENCY 1000
> > Info: BINARY RESTART FILES WILL BE USED
> > Info: CUTOFF 12
> > Info: PAIRLIST DISTANCE 12
> > Info: PAIRLIST SHRINK RATE 0.01
> > Info: PAIRLIST GROW RATE 0.01
> > Info: PAIRLIST TRIGGER 0.3
> > Info: PAIRLISTS PER CYCLE 2
> > Info: PAIRLISTS ENABLED
> > Info: MARGIN 0
> > Info: HYDROGEN GROUP CUTOFF 2.5
> > Info: PATCH DIMENSION 14.5
> > Info: ENERGY OUTPUT STEPS 1000
> > Info: CROSSTERM ENERGY INCLUDED IN DIHEDRAL
> > Info: MOMENTUM OUTPUT STEPS 1000
> > Info: TIMING OUTPUT STEPS 1000
> > Info: PRESSURE OUTPUT STEPS 1000
> > Info: CONJUGATE GRADIENT MINIMIZATION ACTIVE
> > Info: LINE MINIMIZATION GOAL = 0.001
> > Info: BABY STEP SIZE = 0.01
> > Info: TINY STEP SIZE = 1e-06
> > Info: PARTICLE MESH EWALD (PME) ACTIVE
> > Info: PME TOLERANCE 1e-06
> > Info: PME EWALD COEFFICIENT 0.257952
> > Info: PME INTERPOLATION ORDER 4
> > Info: PME GRID DIMENSIONS 84 70 60
> > Info: PME MAXIMUM GRID SPACING 1.5
> > Info: Attempting to read FFTW data from FFTW_NAMD_2.7b2_Linux-x86_64.txt
> > Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
> > Info: Writing FFTW data to FFTW_NAMD_2.7b2_Linux-x86_64.txt
> > Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 2
> > Info: USING VERLET I (r-RESPA) MTS SCHEME.
> > Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
> > Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
> > Info: RIGID BONDS TO HYDROGEN : ALL
> > Info: ERROR TOLERANCE : 1e-05
> > Info: MAX ITERATIONS : 100
> > Info: RIGID WATER USING SETTLE ALGORITHM
> > Info: RANDOM NUMBER SEED 1276619587
> > Info: USE HYDROGEN BONDS? NO
> > Info: Using AMBER format force field!
> > Info: AMBER PARM FILE 1hjn3.prmtop
> > Info: AMBER COORDINATE FILE em2.rst
> > Info: Exclusions will be read from PARM file!
> > Info: SCNB (VDW SCALING) 2
> > Info: USING ARITHMETIC MEAN TO COMBINE L-J SIGMA PARAMETERS
> > Reading parm file (1hjn3.prmtop) ...
> > PARM file in AMBER 7 format
> > Warning: Encounter 10-12 H-bond term
> > Warning: Found 9992 H-H bonds.
> > Info: SUMMARY OF PARAMETERS:
> > Info: 35 BONDS
> > Info: 66 ANGLES
> > Info: 35 DIHEDRAL
> > Info: 0 IMPROPER
> > Info: 0 CROSSTERM
> > Info: 0 VDW
> > Info: 153 VDW_PAIRS
> > Info: TIME FOR READING PDB FILE: 3.8147e-06
> > Info:
> > Info: ****************************
> > Info: STRUCTURE SUMMARY:
> > Info: 31682 ATOMS
> > Info: 31700 BONDS
> > Info: 3068 ANGLES
> > Info: 5926 DIHEDRALS
> > Info: 0 IMPROPERS
> > Info: 0 CROSSTERMS
> > Info: 39178 EXCLUSIONS
> > Info: 30797 RIGID BONDS
> > Info: 64246 DEGREES OF FREEDOM
> > Info: 10877 HYDROGEN GROUPS
> > Info: TOTAL MASS = 192680 amu
> > Info: TOTAL CHARGE = -3.4658e-06 e
> > Info: MASS DENSITY = 0.901939 g/cm^3
> > Info: ATOM DENSITY = 0.0893087 atoms/A^3
> > Info: *****************************
> > Info:
> > Info: Entering startup at 0.150035 s, 9.55043 MB of memory in use
> > Info: Startup phase 0 took 2.5034e-05 s, 9.55052 MB of memory in use
> > Segmentation fault
> >
>
> *******************************
> Thomas C. Bishop
> Tel: 504-862-3370
> Fax: 504-862-8392
> http://dna.ccs.tulane.edu
> ********************************
>
>

-- 
Cordiali saluti, Dr.Oteri Francesco

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