Re: [AMBER] Calcium possibly replaced by carbon with MCPB

From: Pengfei Li <>
Date: Wed, 15 Oct 2014 00:17:05 -0400

Hi Manuel,

No problem. Can you send me the input pdb file (C10_hydrated_fixed_H.pdb) you used in the MCPB script? I can try the total script to further check what is wrong (since I have not gotten the input pdb file, the former
advice I have given to you is mainly based on guess).

All the best,

On Oct 14, 2014, at 9:25 PM, wrote:

> Hi Peng Fei,
> Ok, so I continue to have the same problem... I modified the metals.xml and metalParm.xml files, but I got the same result.
> I also tried to use the metals2.xml and metalParm2.xml files, which contain your updates VDW parameters, also to no avail. I then went on to modify those files in the same way as the metals.xml and metalParm.xml... also no result.
> I also tried to modify the elements.xml and parm94 or 99.xml files, to change all mention of Ca (calcium) to C0, but I got the same result... I really don't know what is happening, and would really appreciate some more help from you.
> Thanks again,
> Manuel
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Received on Tue Oct 14 2014 - 21:30:03 PDT
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