AMBER Archive (2006)

Subject: Re: AMBER: minimization with my own charges

From: Myunggi Yi (myunggi_at_gmail.com)
Date: Thu Aug 31 2006 - 17:22:08 CDT

My resdiues are nomal amino acids.
Their charges charges are slightl different from the orignal one.
I'm looking for the simplest way.

On 8/31/06, Ilyas Yildirim <yildirim_at_pas.rochester.edu> wrote:
> 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 - -
> - Hutchison Hall, # B10 - -
> - Rochester, NY 14627-0216 - Ph.:(585) 275 67 66 (Office) -
> - http://www.pas.rochester.edu/~yildirim/ -
> ---------------------------------------------------------------
>
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-- 
Best wishes,

MYUNGGI YI
==================================
KLB 419
Institute of Molecular Biophysics
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334
http://www.scs.fsu.edu/~myunggi
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