Re: [AMBER] tleap and sander minimization

From: Ben Roberts <>
Date: Thu, 29 Jul 2010 14:52:06 -0400

Hi Lamees,

On 29/7/2010, at 2:35 p.m., Hegazy,Lamees wrote:

> Dear Amber users,
> Iam preparing my protein for molecular dynamics simulations. In my
> first step I used tleap to get the parameter and topology files
> and the new pdb structure which I made from these files using
> ambpdb command has completely different coordinates than the
> original pdb structure.

This may not be a problem. Your system may have been wrapped, or
atoms could have been re-ordered. Have you done a superposition
using something like VMD or PyMol?

> The same happened with minimization using Sander. The resulting
> minimized strucure has completely different coordinates than the
> one I used before minimization. Are these issuea bugs in the
> program or am I doing something wrong.

After a minimisation, you can expect coordinates to have changed.



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Received on Thu Jul 29 2010 - 12:00:35 PDT
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