Re: Problem in running constant pH NAMD job

From: Brian Radak (brian.radak_at_gmail.com)
Date: Sat Aug 14 2021 - 10:22:16 CDT

There's unlikely to be anything wrong with your psf. The flag indicates
that you are specifying too many/few arguments, likely to
cphNumstepsPerSwitch. I would double check that you don't have any stray
characters on that line -- for example, you /cannot/ put comments on the
same line as keywords. I'm not even sure this works with semicolons.

On 8/14/21 10:24 AM, Diship Srivastava wrote:
> 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.
>
> https://urldefense.com/v3/__https://www.dropbox.com/sh/9mdtoabtgnmh0ca/AAA29qDi_a2sj9LYUgdTeN_Va?dl=0__;!!DZ3fjg!psF_-aD-q0gkSvrWh-N8Tp86FmHDHM_WORQgrHi0HDAs1gKAEM2Q4dUdAbfJ3GNmZg$
> <https://urldefense.com/v3/__https://www.dropbox.com/sh/9mdtoabtgnmh0ca/AAA29qDi_a2sj9LYUgdTeN_Va?dl=0__;!!DZ3fjg!psF_-aD-q0gkSvrWh-N8Tp86FmHDHM_WORQgrHi0HDAs1gKAEM2Q4dUdAbfJ3GNmZg$ >
>
> On Thu, 12 Aug 2021 at 22:59, Brian Radak <brian.radak_at_gmail.com
> <mailto: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 <mailto: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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