[AMBER] deselect residues for step1 model in MCPB.py

From: SARAH JEANNE LEFAVE <s.lefave.utah.edu>
Date: Wed, 29 May 2019 16:39:30 +0000

Hi all,

I am working through parameterizing a HEME and Cu using MCPB.py and when building the models during step 1 of the MCPB.py process, there are two residues that are recognized at being side-chain coordinated that are not actually coordinated to the metal. Is there a way to manually set those residues and non binding?

I have reduced the cut-off value to 1 and added the “additional_resids” flag to ensure that the two histidine are coordinated but MCPB always includes a pesky glycine.


input file

original_pdb original.pdb
group_name hemeb
software_version g09
cutoff 1
ion_ids 18564
ion_mol2files ../mol2/FEB.mol2
naa_mol2files ../HEM.mol2
frcmod_files ../HEM.frcmod
additional_resids 106 421

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Received on Wed May 29 2019 - 10:00:03 PDT
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