ERROR: syntax error in file "parameters", line number 15733: syntax error in CHARMM nbfix

[vas2201]

i am getting following error while running the equilibration phase please suggest the fix this error.

#
# ACEMD version 3.7.3
#
# Copyright (C) 2017-2024 Acellera (www.acellera.com)
#
# By using ACEMD, you accept the terms and conditions of the ACEMD licence
# Check the licence by running "acemd --licence"
# More details: https://software.acellera.com/acemd/licence.html
#
# When publishing, please cite:
#   ACEMD: Accelerating Biomolecular Dynamics in the Microsecond Time Scale
#   M. J. Harvey, G. Giupponi and G. De Fabritiis,
#   J Chem. Theory. Comput. 2009 5(6), pp1632-1639
#   DOI: 10.1021/ct9000685
#
# Arguments:
#   input: input
#   platform: 
#   device: 
#   ncpus: 
#   precision: mixed
#
# Licence:
#   Product: ACEMD 3.0
#   Check floating licence:
#     ACELLERA_LICENCE_SERVER -- not defined
#     ACELLERA_LICENSE_SERVER -- not defined
#   Check node-locked licence:
#     ACELLERA_LICENCE_FILE -- not defined
#     ACELLERA_LICENSE_FILE -- not defined
#     /opt/acellera/licence.dat -- DENIED (Unable to locate target file)
#     /opt/acellera/license.dat -- DENIED (Unable to locate target file)
#     /home/nmrbox/spenumutchu/.acellera/licence.dat -- DENIED (Unable to locate target file)
#     /home/nmrbox/spenumutchu/.acellera/license.dat -- DENIED (Unable to locate target file)
#
# WARNING: This ACEMD version expires in 3433 days!
#
# Initialize Python
#   Version: 3.10.8
#   Internal modules: /home/nmrbox/spenumutchu/anaconda3/envs/htmd/lib/acemd/python
#
ERROR: syntax error in file "parameters", line number 15733: syntax error in CHARMM nbfix
ERROR: /home/user/mambaforge/conda-bld/acemd_1704215649797/work/src/mdsim/forcefield.cpp line 160: Cannot read: parameters
# Parse input
#   File name: input
# Format: old
#
# Parse force field and topology files
#   Force field: CHARMM
#   PRM file: parameters

[stefdoerr]

Hi, there is an issue with the CHARMM builder of HTMD. When attempting to merge multiple CHARMM parameter files into a single one it's failing due to some repeated entries. If you go to the syntax error line which it reports you can probably comment it out and it should go forward. If you need more help send me the equilibration folder and I can take a look at it

[tonigi]

It may be due to code lines like these...

! features to be added to CHARMM.
! parallel fix, to avoid duplicated messages in the log
set para
if ?NUMNODE gt 1 set para node 0

set wrn ?WRNLEV
! Some versions of CHARMM don't seem to initialize wrnlev...
if "@WRN" eq "?WRNLEV" set wrn 5

...likely unprocessed stream files. Line 15733 with the default charmm topo/parm is set para indeed.

[tonigi]

Kludged as follows:

--- parameters.old	2024-10-31 19:00:02.000000000 +0100
+++ parameters	2024-10-31 19:05:36.000000000 +0100
@@ -15730,12 +15730,12 @@
 ! want the NBFixes to apply. A more elegant solution would require new
 ! features to be added to CHARMM.
 ! parallel fix, to avoid duplicated messages in the log
-set para
-if ?NUMNODE gt 1 set para node 0
+!set para
+!if ?NUMNODE gt 1 set para node 0

-set wrn ?WRNLEV
+!set wrn ?WRNLEV
 ! Some versions of CHARMM don't seem to initialize wrnlev...
-if "@WRN" eq "?WRNLEV" set wrn 5
+!if "@WRN" eq "?WRNLEV" set wrn 5
 !Following lines added from par_all36_cgenff.prm
 !!! IMPORTANT!!!
 !!! The following topology & parameter files should be read before reading top_all36_cgenff.rtf/par_all36_cgenff.prm

[stefdoerr]

I've fixed the issue on main branch but I'm currently fighting some failing tests on Windows before making a new release.

[stefdoerr]

Ok the new version 2.4.1 which fixes this is out now for every platform except Linux python 3.11. So I will close the issue for now as that specific build depends on the upcoming ACEMD4 release.