Yes, I did superposition and the tleap structure completely
superimposed on the original structure . the same with the
minimzed structure, it has totaly transformed coordinates but when
I superimosed it on the original structure, it has only slight
change as expected.
On Thu Jul 29 14:52:06 EDT 2010, Ben Roberts <roberts.qtp.ufl.edu>
wrote:
> 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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--
Hegazy,Lamees
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Received on Thu Jul 29 2010 - 12:30:03 PDT
