From: Michel Espinoza-Fonseca (mef_at_ddt.biochem.umn.edu)
Date: Sat Apr 09 2005 - 20:31:18 CDT
Hm.... I guess the problem is then related to the parameter file... I'm
not sure about this atom (I'm not a force field developer), but can you
attach the original system you are using?
Michel
-----Original Message-----
From: Baoqiang Cao [mailto:caobg_at_email.uc.edu]
Sent: Saturday, April 09, 2005 9:26 PM
To: Michel Espinoza-Fonseca; namd-l_at_ks.uiuc.edu
Subject: Re: RE: namd-l: error: UNABLE TO FIND ANGLE PARAMETERS FOR C
NH1 C
Hello Michel,
Thanks! But I faced another weird problem...
The version using is 2.5 (Linux-i686).
I even tried use the original pdb files downloaded from the tuturioal
websited you mentioned, in that, I suspect something ridiculously wrong
with my namd2. Any comments will be highly appreciated! Thanks.
See below for the detailed log file, please.
======= At 2005-04-09, 16:41:45 you wrote: =======
>Why you don't try this link:
>
>http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/
>
>There you can find a nice example on how build and perform a MD
>simulation including a lipid bilayer.
>
Charm++: standalone mode (not using charmrun)
Info: NAMD 2.5 for Linux-i686
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: Based on Charm++/Converse 050612 for net-linux-icc
Info: Built Fri Sep 26 17:33:59 CDT 2003 by jim on lisboa.ks.uiuc.edu
Info: Sending usage information to NAMD developers via UDP. Sent data
is:
Info: 1 NAMD 2.5 Linux-i686 1 ***.cinci.rr.com bqcao
Info: Running on 1 processors.
Info: 1335 kB of memory in use.
Measuring processor speeds... Done.
Info: Configuration file is equil.namd
TCL: Suspending until startup complete.
Info: SIMULATION PARAMETERS:
Info: TIMESTEP 1
Info: NUMBER OF STEPS 0
Info: STEPS PER CYCLE 20
Info: PERIODIC CELL BASIS 1 30 0 0
Info: PERIODIC CELL BASIS 2 15 25.98 0
Info: PERIODIC CELL BASIS 3 0 0 64
Info: PERIODIC CELL CENTER 0 0 0
Info: WRAPPING ALL CLUSTERS AROUND PERIODIC BOUNDARIES ON OUTPUT.
Info: WRAPPING TO IMAGE NEAREST TO PERIODIC CELL CENTER.
Info: LOAD BALANCE STRATEGY Other
Info: LDB PERIOD 4000 steps
Info: FIRST LDB TIMESTEP 100
Info: LDB BACKGROUND SCALING 1
Info: HOM BACKGROUND SCALING 1
Info: PME BACKGROUND SCALING 1
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: DCD FILENAME equil_out.dcd
Info: DCD FREQUENCY 100
Warning: INITIAL COORDINATES WILL NOT BE WRITTEN TO DCD FILE
Info: XST FILENAME equil_out.xst
Info: XST FREQUENCY 100
Info: NO VELOCITY DCD OUTPUT
Info: OUTPUT FILENAME equil_out
Info: NO RESTART FILE
Info: SWITCHING ACTIVE
Info: SWITCHING ON 8.5
Info: SWITCHING OFF 10
Info: PAIRLIST DISTANCE 11.5
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 5
Info: HYDROGEN GROUP CUTOFF 2.5
Info: PATCH DIMENSION 19
Info: ENERGY OUTPUT STEPS 10
Info: TIMING OUTPUT STEPS 100
Info: FIXED ATOMS ACTIVE
Info: FORCES BETWEEN FIXED ATOMS ARE CALCULATED
Info: HARMONIC CONSTRAINTS ACTIVE
Info: HARMONIC CONS EXP 2
Info: LANGEVIN DYNAMICS ACTIVE
Info: LANGEVIN TEMPERATURE 310
Info: LANGEVIN DAMPING COEFFICIENT IS 10 INVERSE PS
Info: LANGEVIN DYNAMICS NOT APPLIED TO HYDROGENS
Info: LANGEVIN PISTON PRESSURE CONTROL ACTIVE
Info: TARGET PRESSURE IS 1.01325 BAR
Info: OSCILLATION PERIOD IS 200 FS
Info: DECAY TIME IS 100 FS
Info: PISTON TEMPERATURE IS 310 K
Info: PRESSURE CONTROL IS GROUP-BASED
Info: INITIAL STRAIN RATE IS 0 0 0
Info: CELL FLUCTUATION IS ANISOTROPIC
Info: SHAPE OF CELL IS CONSTRAINED IN X-Y PLANE
Info: PARTICLE MESH EWALD (PME) ACTIVE
Info: PME TOLERANCE 1e-06
Info: PME EWALD COEFFICIENT 0.312341
Info: PME INTERPOLATION ORDER 4
Info: PME GRID DIMENSIONS 32 32 64
Info: Attempting to read FFTW data from FFTW_NAMD_2.5_Linux-i686.txt
Info: Optimizing 6 FFT steps. 1... 2... 3... 4... 5... 6... Done.
Info: Writing FFTW data to FFTW_NAMD_2.5_Linux-i686.txt
Info: FULL ELECTROSTATIC EVALUATION FREQUENCY 4
Info: USING VERLET I (r-RESPA) MTS SCHEME.
Info: C1 SPLITTING OF LONG RANGE ELECTROSTATICS
Info: PLACING ATOMS IN PATCHES BY HYDROGEN GROUPS
Info: NONBONDED FORCES EVALUATED EVERY 2 STEPS
Info: RANDOM NUMBER SEED 1113095679
Info: USE HYDROGEN BONDS? NO
Info: COORDINATE PDB grama.pdb
Info: STRUCTURE FILE grama.psf
Info: PARAMETER file: CHARMM format!
Info: PARAMETERS par_all27_prot_lipid.inp
Info: PARAMETERS par-extraterms.inp
Info: SUMMARY OF PARAMETERS:
Info: 179 BONDS
Info: 443 ANGLES
Info: 537 DIHEDRAL
Info: 49 IMPROPER
Info: 89 VDW
Info: 0 VDW_PAIRS
FATAL ERROR: CAN'T FIND BOND PARAMETERS FOR BOND C - NH3L IN PARAMETER
FILES
Stack Traceback:
[0] _ZN10Parameters17assign_bond_indexEPcS0_P4bond+0xf2 [0x8206a02]
[1] _ZN8Molecule10read_bondsEP8_IO_FILEP10Parameters+0x179
[0x81e95fd]
[2] _ZN8Molecule13read_psf_fileEPcP10Parameters+0x36f [0x81e82af]
[3] _ZN8MoleculeC2EP13SimParametersP10ParametersPc+0x6b [0x81e7eec]
[4] _ZN9NamdState14configListInitEP10ConfigList+0x6ad [0x81fb88d]
[5] _ZN9ScriptTcl9initcheckEv+0x59 [0x822b1a1]
[6] _ZN9ScriptTcl12Tcl_minimizeEPvP10Tcl_InterpiPPc+0x1e [0x8229412]
[7] TclInvokeStringCommand+0x6d [0x82c5145]
[8] ./namd2 [0x82f946a]
[9] Tcl_EvalEx+0x1cc [0x82f9b7c]
[10] Tcl_EvalFile+0x157 [0x82f1ce3]
[11] _ZN9ScriptTcl3runEPc+0x1a [0x8228b76]
[12] main+0x1d2 [0x80ed052]
[13] __libc_start_main+0xe3 [0x98fe33]
[14] sinh+0x65 [0x80eaed1]
>Hope it works,
>Peace
>Michel
>
>-----Original Message-----
>From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On
>Behalf Of Baoqiang Cao
>Sent: Saturday, April 09, 2005 2:41 PM
>To: namd-l_at_ks.uiuc.edu
>Subject: namd-l: error: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C
>
>Hi All,
>
>First of all, thanks Xiaoqing and Leandro for the previous
>scripts inquiring message.
>
>Following
>http://mccammon.ucsd.edu/~rlaw/ctbp_workshop_rlaw.htm , I was
>trying to minimize a membrane+protein+water+ion system with
>using glycoph_min.in on the website, the error message I got is:
>
>Reason: FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C
>Charm++ fatal error:
>FATAL ERROR: UNABLE TO FIND ANGLE PARAMETERS FOR C NH1 C
>
>Aborted
>
>Could any body show me what went wrong? BTW: Did anybody
>actually try them before? Any tips will be welcome!
>
>Thanks.
>
>Best,
> Baoqiang Cao
= = = = = = = = = = = = = = = = = = = =
Baoqiang Cao
caobg_at_email.uc.edu
2005-04-09
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