AMBER Archive (2006)

Subject: Re: AMBER: minimization with my own charges

From: Ilyas Yildirim (
Date: Thu Aug 31 2006 - 17:12:24 CDT

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.


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
  - Department of Chemisty       -				-
  - University of Rochester      -				-
  - Hutchison Hall, # B10        -				-
  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  -			-

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