From: Diship Srivastava (dishipsrivastava_at_gmail.com)
Date: Wed Aug 11 2021 - 11:02:32 CDT
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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