From: Baoqiang Cao (caobg_at_email.uc.edu)
Date: Sat Apr 09 2005 - 22:46:44 CDT
Hello Michel,
What I used are, from http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on/sample/
fix_backbone.pdb
restrain_ca.pdb
equil.namd
I think they are supposed to work very well since they are samples, my wrong wherever doings...
My machine is runing FC3, any thing else you need? Thanks!
Best,
Baoqiang Cao
Best regards,
======= At 2005-04-09, 20:31:18 you wrote: =======
>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
= = = = = = = = = = = = = = = = = = = =
Baoqiang Cao
caobg_at_email.uc.edu
2005-04-09
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:39:20 CST