Re: [AMBER] Unwanted water protein interaction

From: David A Case <>
Date: Sun, 17 Oct 2021 06:30:08 -0400

On Sat, Oct 16, 2021, mohamed marzouk wrote:

>During preparation of top file by tleap for protein/DNA complex some fat
>water molecules interact with protein!!! Attached photos for vmd and pdb

You should look at your input pdb file, especially for residues 1000 and
1003, etc. Also, look carefully in the leap.log file for any messages that
look odd. You could try to create a small example that illustrates the
problem, but it seems likely that there is something amiss with your input


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Received on Sun Oct 17 2021 - 04:00:02 PDT
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