Re: [AMBER] MCPB problems

From: Pengfei Li <>
Date: Tue, 1 Nov 2016 11:16:21 -0500

Hi Fabrico,

The problem could be about the wrong total charge during the RESP charge fitting.

Which means when calculate the total charge by itself it adds up the partial charges in the database and mol2 files you created. This may be different from the actual charge of the system.

The quick way to solve this problem is to add “lgmodel_chg" keyword to define the large model total charge by yourself and then perform the third step modeling of again.

Please let me know whether it works.

Kind regards,

> On Nov 1, 2016, at 9:58 AM, Fabrício Bracht <> wrote:
> Hi Pengfei. I recently had to redo a parameterization in order to get the
> original mol2 files. I had to do this because my computer was stolen and on
> the cluster I only had the topology files.
> Although I used the exact same files, now I get charges that are sometimes
> very different. For example charges of 2.84 on a CT atom and -1.95 on a CR
> atom.
> I have encountered a similar problem while trying to parameterize a new
> system which included a ligand. First I thought it was something related to
> the gaussian calculation, but when the same thing happened to the system I
> had already worked on, I figured something might be off.
> I am using the release2 version of because it seems to be the only
> one that recognizes a N terminal histidine as NHIC (which is one of the
> residues that binds to the metal atom).
> Any ideas?
> Thanks
> Fabrício
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Received on Tue Nov 01 2016 - 09:30:03 PDT
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