[AMBER] MCPB problems

From: Fabrício Bracht <fabracht1.gmail.com>
Date: Tue, 1 Nov 2016 12:58:42 -0200

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
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 MCPB.py 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?
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Received on Tue Nov 01 2016 - 08:00:02 PDT
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