Re: [AMBER] Water do not see the system....

From: David A Case <>
Date: Wed, 10 Oct 2018 16:16:03 -0400

On Wed, Oct 10, 2018, Vito GENNA wrote:

> Once i got the system I minimize it and what I note is that water molecules
> dramatically overlap protein's atoms.

What is the evidence that this is happening? Did you visualize the
system? Calculate the distance from a given water molecule to a given
protein atom? Something else?

You can use the "checkoverlap" command in cpptraj to print out all short
contacts. There should be very few of these following minimization. It
would probably also be more helpful to see the *output* from
minimization, rather than the input file.

Look carefully at the minimization and heating outputs for evidence of
problems. It looks like you have 750 residues in your protein: is that
correct? You might try a short calculation on a smaller fragment. I
didn't notice anything wrong with your tleap input, but I could be
missing something.


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Received on Wed Oct 10 2018 - 13:30:02 PDT
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