Re: [AMBER] Unwanted water protein interaction

From: mohamed marzouk <>
Date: Sun, 17 Oct 2021 19:34:20 +0900

Thank you,
I have checked these atoms but nothing strange in them.
Then I applied the Minimization for this files and all unwanted clashes solved and now the system is stable.
I think this is okay to equilibrate the system then, isn’t it?

Best regards,
Mohamed Marzouk Sobeh
Ph.D student at Life Science and Technology, Tokyo Institute of Technology, Tokyo, Japan.
T.A Physics department,Ain Shams University, Cairo, Egypt.

Mob. and WhatsApp.:
               +81 070-4070-9549
                +2 01061417414

> On Reiwa 3 Oct 17, at 19:30, David A Case <> wrote:
> 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
>> file
> 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
> file.
> ....dac
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Received on Sun Oct 17 2021 - 04:00:02 PDT
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