Dear Myunggi,
Do u have the new residue library, which includes your charges? If yes, u
should create the prmtop and inpcrd files in xleap using this library for
your structure. U will use the normal sander program of AMBER 9 if u want
to minimize the structure. If u are not using the Thermodynamic
Integration Approach, sander is not different (just for the records, if u
want to do TI calculation, u need to use sander.MPI in AMBER 9, which is
running sander in parallel mode). Good luck.
Best,
On Thu, 31 Aug 2006, Myunggi Yi wrote:
> Dear Amber users,
>
> I want to minimize a structure with my own charges for some residues.
> I think a simple way to assign my charges is using free energy perturbation.
>
> I don't want the free energy calculation.
> I will do only minimization with the perturbed charges.
>
> It seems amber 9 is different from amber 7.
>
> Would you suggest some idea?
>
>
>
--
Ilyas Yildirim
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- http://www.pas.rochester.edu/~yildirim/ -
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Received on Sun Sep 03 2006 - 06:07:16 PDT
