Dear all,
I'm trying to use MCPB.py on a complex with two Mn3+ and two Mn4+, 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-CA as normal.
It contains the residue 1132-MN1 as normal.
It contains the residue 1133-MN2 as normal.
It contains the residue 1134-MN3 as normal.
It contains the residue 1135-MN4 as normal.
It contains the residue 1136-O1 as normal.
It contains the residue 1137-O2 as normal.
It contains the residue 1138-O3 as normal.
It contains the residue 1139-O4 as normal.
It contains the residue 1140-O5 as normal.
It contains the residue 1155-WAT as normal.
It contains the residue 1183-WAT as normal.
It contains the residue 1214-WAT as normal.
It contains the residue 1225-WAT as normal.
Totally there are 103 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'
Attached are related files and the operation video.
Thanks and Regards,
Song
从网易企业邮箱发来的云附件
oec_Mn3.rar
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oec_Mn3_video.rar
83.93M | 过期时间：2022年7月15日 15:22
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Received on Thu Aug 04 2022 - 13:33:52 PDT
