Hello,
You have really not provided enough information for us to help you
track down the problem. There are many reasons why the GBTOT and
PBTOT may be too high. I believe the program that prepares the
snapshots automatically mutates the selected residue(s) to an alanine.
However, you do have to provide mutant topology files as well. Are
you sure that you created compatible prmtops? Have you gotten the
tutorials to work for you? (i.e. reproduced the results obtained on
the tutorial?)
Good luck!
Jason
On Sat, Jan 2, 2010 at 3:48 AM, Maryam Hamzehee <maryam_h_7860.yahoo.com> wrote:
>
> Dear All
> I am doing the alanine screening method using MM-PBSA method as implemented in AMBER 9 to calculate the binding free energy for the association of two proteins.
> In ADVANCED TUTORIALS TUTORIAL 3 (MM-PBSA) we have to perform a seperate MD simulation of the mutated form of structures; subsequently, binding free energy can be calculated for complex of two proteins.
> In order to save time, I would like to obtain several snapshots of mutated form of structures from the wild-type trajectory by atomic coordinate removal and calculate the binding energy so in this way it is assumed there is no significant structural change upon mutation.
> I performed the mutation and calculate the binding energy using the trajectory of wild type of complex of protein. It was observed that the values for calculated GBTOT and PBTOT were too high (for example 2526564) I think there is something wrong with this method,
> I would be grateful if some one help me in this regard.
>
> Best regards,
> Maryam
>
>
>
>
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>
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jan 02 2010 - 06:30:03 PST
