Re: [AMBER] Ligand and receptor separated when setting iwrap=1

From: Brian Radak <radak004.umn.edu>
Date: Sun, 8 Apr 2012 14:48:55 -0400

Hi Denis,

I believe you are looking for functionality contained in the ptraj program,
which is part of AmberTools. Specifically, you probably want the "image"
and "center" commands. Both of these are well documented in the
AmberTools12 manual.

Regards,
Brian

On Sun, Apr 8, 2012 at 10:39 AM, Liu Denis <cndenis.gmail.com> wrote:

> Dear Amber friends,
>
> I used iwrap=1 in a long MD run, it caused the ligand "jump" to the other
> side of periodic box and separated from the receptor. The RMSD also jump
> from 3 to 20.
>
> How to "un-wrap" and put the ligand back to the receptor after MD
> simulation?
>
> Thanks!
> Denis
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 



-- 
================================ Current Address =======================
 Brian Radak                                             :     BioMaPS
Institute for Quantitative Biology
 PhD candidate - York Research Group       :     Rutgers, The State
University of New Jersey
 University of Minnesota - Twin Cities         :     Center for Integrative
Proteomics Room 308
 Graduate Program in Chemical Physics     :     174 Frelinghuysen Road,
 Department of Chemistry                          :     Piscataway, NJ
08854-8066
 radak004.umn.edu                                 :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Apr 08 2012 - 12:00:03 PDT
Custom Search