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.
Regards,
Ben
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Received on Thu Jul 29 2010 - 12:00:35 PDT
