Re: [AMBER] Problem regarding Same coordinate for two atoms

From: Jason Swails <>
Date: Sat, 22 Jan 2011 02:14:35 -0500


You should run a short minimization on your system before you try to run any
molecular dynamics. This is the best way to relieve these bad contacts.

After that, you should carefully heat up your system before running your
production dynamics.

I hope this helps,

On Sat, Jan 22, 2011 at 1:34 AM, Hirdesh Kumar <>wrote:

> Hi Amber Users,
> I am trying to heat my protein ligand complex at constant volume. But it is
> showing SHAKE error. I googled the error and found that it is due to
> overlap
> of the coordinate. I tested the same using ptraj close contact utility. I
> generated the .pdb file from the .parm7 and .rst file and change the
> coordinate of overlapping hydrogen. But Now I am stuck how to convert my
> protein (*.pdb format*) back into the .parm7 and .crd file. One option is
> by
> using tleap again on my complex, but for that I need the parameter file for
> my solvent molecule (i.e. TIP3P). Is there any other option for the same??
> Thanks and Regard,
> Hirdesh
> _______________________________________________
> AMBER mailing list

Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
AMBER mailing list
Received on Fri Jan 21 2011 - 23:30:04 PST
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