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Acellera / htmd

HTMD: Programming Environment for Molecular Discovery
https://software.acellera.com/docs/latest/htmd/index.html
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ERROR: syntax error in file "parameters", line number 15733: syntax error in CHARMM nbfix #1093

Open vas2201 opened 2 months ago

vas2201 commented 2 months ago

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 commented 1 month ago

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