AMBER Archive (2006)

Subject: Re: AMBER: minimization with my own charges

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
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.

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
  ---------------------------------------------------------------
  - Department of Chemisty       -				-
  - University of Rochester      -				-
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  - Rochester, NY 14627-0216     - Ph.:(585) 275 67 66 (Office)	-
  - http://www.pas.rochester.edu/~yildirim/			-
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