Dear all,
I'm trying to use MCPB.py on a complex with four Mn3+ , but when entering the
command "MCPB.py -i 3wu2.in -s 1" I get an error as shown below.
How can I fix this error? I don't know how to set the atom name and Residue name in the pdb files，
when there are four Mn ions at the same time, whether the valence state is different and the naming is different,
such as As3+，its Residue name is“ARS”, and its atom name is“AS".
The error message is as follows:
It contains the residue 1131-MN1 as normal.
It contains the residue 1132-MN2 as normal.
It contains the residue 1133-MN3 as normal.
It contains the residue 1134-MN4 as normal.
......
Totally there are 155 atoms in the small model.
Traceback (most recent call last):
File "/opt/amber20/bin/MCPB.py", line 643, in <module>
gene_model_files(orpdbf, ionids, addres, addbpairs, gname, ff_choice,
File "/opt/amber20/lib/python3.8/site-packages/pymsmt/mcpb/gene_model_files.py", line 1902, in gene_model_files
build_small_model(mol, reslist, ionids, cutoff, smresids, smresace, smresnme,
File "/opt/amber20/lib/python3.8/site-packages/pymsmt/mcpb/gene_model_files.py", line 1380, in build_small_model
AtNum = Atnum[gatm.element]
KeyError: 'M'
Thanks and Regards,
Song
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Aug 04 2022 - 13:33:30 PDT
