From: Brian Radak (brian.radak_at_gmail.com)
Date: Thu Aug 12 2021 - 12:29:25 CDT
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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