[AMBER] MCPB.py error on first step.

From: DE-SANTANA-PONTES, FREDERICO J. via AMBER <amber.ambermd.org>
Date: Tue, 24 Jan 2023 15:03:21 +0000

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,

AMBER mailing list
Received on Tue Jan 24 2023 - 07:30:03 PST
Custom Search