Hi Everyone!
It's my first experience using AMBER to develop nonstandard parameters. I'm working with some organometallic compounds (Tin as a central atom and coordinated by organic ligands and two chloride atoms) and decided to use MCPB.py to obtain force field parameters for my molecules. I had a problem at first step using MCPB.py
MCPB.py -i DPhT.in -s 1
My in file is
original_pdb DPhT.pdb
group_name DPhT
ion_ids 1
ion_mol2files DPhT_only_SN.mol2
naa_mol2files Chloride.mol2 Phenyl.mol2
frcmod_files Chloride.frcmod Phenyl.frcmod
I checked the atom's name in each mol2 and pdb files and they are the same, frcmod and mol2 have also the same name. However, I got the following error:
Traceback (most recent call last):
File "/home/fpontes/miniconda3/envs/AmberTools22/bin/MCPB.py", line 651, in <module>
gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
File "/home/fpontes/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/pymsmt/mcpb/gene_model_files.py", line 1906, in gene_model_files
build_standard_model(mol, reslist, cutoff, msresids, outf, ionids,
File "/home/fpontes/miniconda3/envs/AmberTools22/lib/python3.10/site-packages/pymsmt/mcpb/gene_model_files.py", line 1471, in build_standard_model
attype = libdict[resname + '-' + atname][0]
KeyError: 'UNL-CL'
Could someone help me to solve this error?
Thanks in advance,
Fred
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Received on Tue Jan 24 2023 - 07:30:03 PST
