Dear Brian:
Thank you. I have read AmberTool 11 manual, and tried the method
from
http://archive.ambermd.org/200910/0459.html
> center :1-371 mass origin
> image origin center bymask familiar
> center :1-372 mass origin
> image origin center bymask familiar
> Where I am simulating a protein with ligand, and residues 1-371 belong to
> the receptor and the last residue, 372, is the ligand. Adjust accordingly
> for your system. This script has, in the past, properly recentered and
> imaged my trajectories.
I changed the residue number to my residue number and generated a new
trajectory,
but the ligand still jump outside the receptor occasionally.
In another mail, Tom suggested using a modified prmtop in ptraj to put the
complex back,
but he did not provide detail information in mail list. How to do it?
http://archive.ambermd.org/200808/0315.html
> So, I think you can continue with your PMEMD wrapping (i.e. restart from
> the b4 restrt and continue running turning on IWRAP=1) and then later use
> ptraj to put the complex back together again. [e-mail me offline if you
> want to have the prmtop modified so that the protein will never
> "dissociate" to periodic images...]
Best
Denis
2012/4/9 Brian Radak <radak004.umn.edu>
> 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 09 2012 - 00:00:03 PDT
