Distance restraints are probably most easily introduced via the nmropt
command. The section in the manual titled "NMR, X-ray, and cryo-EM/ET
refinement" describes its usage.
Regards,
Brian
On Mon, Sep 30, 2013 at 10:17 AM, Fengxue Li <lifx916.126.com> wrote:
> hi，all
> Iused pmemd implemented in AMBER11 package to run MD，I followed the
> following procedure;
> 1)Minimization Stage 1 - Holding the solute fixed
> 2)Minimization Stage 2 - Minimizing the entire system
> 3)Molecular Dynamics (heating) with restraints on the solute
> 4)Running MD Equilibration on the whole system,but i want to know how to
> run MD in limiting the distance of two specified atoms?
> Can anyone help me to run restricted MD?
> Thank you in advance for you help.
> _______________________________________________
> 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.
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Received on Mon Sep 30 2013 - 09:00:03 PDT
