From: Diship Srivastava (dishipsrivastava_at_gmail.com)
Date: Sat Aug 14 2021 - 09:24:49 CDT
Thanks for the reply.
No I did not used any other keywords. I am attaching my psf and pdb file
in attachment. You can check if I am making some mistake.
On Thu, 12 Aug 2021 at 22:59, Brian Radak <brian.radak_at_gmail.com> wrote:
> I don't see anything wrong from the snippet you posted. Though based on
> the error message one of the commands expected an even number of arguments,
> presumably as a list of labeled values. Are there other relevant keywords
> to show?
>
> BKR
>
> On Wed, Aug 11, 2021, 12:04 PM Diship Srivastava <
> dishipsrivastava_at_gmail.com> wrote:
>
>> Hi,
>> I am trying to do a constant ph namd job on a small protein containing
>> GLU and LYS residues using NAMD2.14. While running namd my job crashes
>> with "FATAL ERROR: TCL: argument list must have multiple of 2 arguments! "
>> just after reading the top_cph36_prot.rtf file. I am following the cph
>> tutorial distributed along with namd2.14.I have completed normal
>> equilibration of the same system using the same configuration file (
>> without consph specific keywords) and using its restart files as input
>> files for position and velocity in current consph job. Any help in solving
>> this problem will be most appreciated.
>>
>> A snippet of my configuration file is as follows :
>> #--------------------------------------------------------------
>> ## constph specific keywords
>> paraTypeCharmm on
>> parameters par_all36_prot.prm
>> parameters toppar_water_ions.str
>> parameters par_cph36_prot.prm
>> # Load constant-pH specific topology files
>> cphConfigFile conf_cph36_prot.json
>> topology top_cph36_prot.rtf
>>
>>
>> set pH 5
>>
>> pH $pH
>> outputname $pH/c6pep_310
>> cphMDBasename $pH/namdcph.md
>> cphSwitchBasename $pH/namdcph.sw
>>
>> # switch at 15ps
>> cphNumstepsPerSwitch 7500
>> # Minimize after randomizing protonation states at start.
>> cphNumMinSteps 100
>> # numsteps = 500 => number of steps of conventional MD to be run in
>> between switches
>> # numcycles = 5000 => number of MC/MD cycles
>> cphRun 500 5000
>>
>> #------------------------------------------------
>>
>> My logfile is as follows:
>>
>> PSFGEN 1.6.7 from NAMD Git-2019-12-01 for Linux-x86_64-multicore
>> psfgen) reading topology file top_cph36_prot.rtf
>>
>> psfgen) > CHARMM36 All-Hydrogen Topology File for Titratable Proteins <
>> psfgen) >>>>>>>>>>>>>>>>>>>>>>>>>> Jun 2017 <<<<<<<<<<<<<<<<<<<<<<<<<<<
>> psfgen) Patches and residues for constant-pH MD in NAMD
>> psfgen)
>> psfgen) Created by CHARMM version 36 1
>> psfgen) cross-term entries present in topology definitions
>> FATAL ERROR: TCL: argument list must have multiple of 2 arguments!
>> ------------- Processor 0 Exiting: Called CmiAbort ------------
>> Reason: FATAL ERROR:
>>
>> TCL: argument list must have multiple of
>> 2 arguments!
>>
>> [0] Stack Traceback:
>> [0:0] namd2 0x4f16c4
>> [0:1] namd2 0xdcf3d7
>> [0:2] namd2 0x1425658 TclInvokeStringCommand
>> [0:3] namd2 0x1428170
>> [0:4] namd2 0x146af53
>> [0:5] namd2 0x14a5cc7
>> [0:6] namd2 0x1428170
>> [0:7] namd2 0x146af53
>> [0:8] namd2 0x14a5cc7
>> [0:9] namd2 0x1428170
>> [0:10] namd2 0x1429556
>> [0:11] namd2 0x1429d36
>> [0:12] namd2 0x148bb41
>> [0:13] namd2 0x148bcfe
>> [0:14] namd2 0xdc2bd0
>> [0:15] namd2 0x50cb80
>> [0:16] libc.so.6 0x7fc6afc20bf7 __libc_start_main
>> [0:17] namd2 0x4118f5
>> CHARM++ FATAL ERROR: FATAL ERROR:
>>
>> TCL: argument list must have
>> multiple of 2 arguments!
>>
>> Segmentation fault (core dumped)
>>
>>
>> --
>> Diship Srivastava
>> JRF
>> Department of Chemistry
>> IIT(ISM) - Dhanbad
>> India
>>
>
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