Hi Sarah,
The information you provided was not enough for me to make a judgement. Can you send me the files that were referenced in your input file in another email? I can help to do a check.
-Pengfei
> On May 29, 2019, at 12:39 PM, SARAH JEANNE LEFAVE <s.lefave.utah.edu> wrote:
>
> 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.
>
> Thanks,
> Sarah
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Jun 01 2019 - 13:00:02 PDT
