VMD-L Mailing List

From: Nick Bayhi (bayhi_at_uchicago.edu)
Date: Fri Jan 07 2022 - 14:19:55 CST

Hello,

I am encountering a problem while trying to run NetworkView using VMD.
While the tutorial's .dcd and .psf run without issue, I'm encountering
errors when I try to run for my simulations or those of my collaborators.

I submit my .dcd and .psf files using the networkSetup network.config
script described in the tutorial, but the two files created by Carma are
essentially empty and I receive the following error:

(common) 18 % networkSetup network.config

line: ../1.network_preparation/ide2zn.psf

./1.network_preparation/ide2zn.psf

./1.network_preparation/ide2zn_ctd.dcd

line: (chain AP1 BP1 )

(chain AP1 BP1 )

line: (name CA)

(name CA)

-code 1 -level 0 -errorcode {CHILDSTATUS 54199 1} -errorinfo {CatDCD 4.0

Reading indices from file 'carma.indices'

Error: no indices found in file.

    while executing

"::exec /home/bayhi/network_programs/catdcd -stride 1 -i carma.indices -o
carma.dcd ../1.network_preparation/ide2zn_ctd.dcd"

    ("eval" body line 1)

    invoked from within

"eval ::exec [list $exec_path] [lrange $args 1 end]"

    (procedure "::ExecTool::exec" line 14)

    invoked from within

"::ExecTool::exec catdcd -stride $stride -i $indexFile -o $outFile
$dcdFileNames"

    ("eval" body line 1)

    invoked from within

"eval ::ExecTool::exec {catdcd -stride $stride -i $indexFile -o $outFile
$dcdFileNames} "} -errorline 13

I'm running on our Linux cluster. I believe I've added the correct carmanox
and catdcd executables to my path correctly (according to online guidance),
but it's possible there's something I've missed there. Below I've copied
the first couple lines of my .psf file, where it's clear that indices are
included, and I'm happy to share any other information if it's helpful.

Thank you for your help!
Nick Bayhi

PSF CMAP

       1 !NTITLE
 REMARKS original generated structure x-plor psf file
 REMARKS 4 patches were applied to the molecule.
 REMARKS topology 8-O_pO-insB_withZn_autopsf-temp.top
 REMARKS segment AP1 { first NTER; last CTER; auto angles dihedrals }
 REMARKS segment BP1 { first NTER; last CTER; auto angles dihedrals }
 REMARKS segment AO1 { first none; last none; auto angles dihedrals }
 REMARKS segment BO1 { first none; last none; auto angles dihedrals }
 REMARKS patch CTER AP1:1011
 REMARKS patch NTER AP1:46
 REMARKS patch CTER BP1:1011
 REMARKS patch NTER BP1:46

   31458 !NATOM
       1 AP1 46 ALA N NH3 -0.300000 14.0070 0
       2 AP1 46 ALA HT1 HC 0.330000 1.0080 0
       3 AP1 46 ALA HT2 HC 0.330000 1.0080 0 

--
Nick Bayhi
(971) 219-7408
Wei-Jen Tang Lab <https://urldefense.com/v3/__https://voices.uchicago.edu/wtang-lab/__;!!DZ3fjg!pdimRyTmTWhtIo5zfj7U0Vb7cxfBd1ck2Z85Bvhp3GDyd6mYBQDDOkM_mBFkXC-BXw$ >
Biophysical Sciences
University of Chicago