I really think you should try the imaging commands in cpptraj. Autoimage is
a good place to start.
On Fri, Jun 1, 2018, 9:15 PM Edjan Silva <edjan.silva.esenfar.ufal.br>
wrote:
> Thanks a lot for the help. The problem may be with the input file settings.
> configurations of a protein - drug simulation were used, with few
> alterations. maybe this is the problem.
>
> 2018-06-01 12:17 GMT-03:00 Carlos Simmerling <carlos.simmerling.gmail.com
> >:
>
> > Centering alone probably won't be enough, because the RMSD routine does a
> > best-fit that will fix any centering problems. The more likely problem is
> > that your complex has been separated by periodic imaging. That's why I
> > suggested checking the archives for imaging, this has been discussed
> before
> > and you should find everything you need to fit it in the archives.
> >
> > On Fri, Jun 1, 2018 at 10:35 AM, ABEL Stephane <Stephane.ABEL.cea.fr>
> > wrote:
> >
> > > Hi,
> > >
> > > You observed this behavior because you DNA-complex is not centered in
> the
> > > box. So you have to center the molecule in the box before to do the
> rmsd
> > > calculation
> > >
> > > HTH
> > >
> > > ________________________________________
> > > De : Edjan Silva [edjan.silva.esenfar.ufal.br]
> > > Envoyé : vendredi 1 juin 2018 16:26
> > > À : AMBER Mailing List
> > > Objet : [AMBER] high values ​​of RMSD during the simulation of
> molecular
> > > dynamics between DNA and small molecule. Does anyone explain?
> > >
> > > I performed a simulation between a small molecule and B-DNA. The result
> > of
> > > the RMSD is this of the figure. By analyzing the structure at these
> > points,
> > > it appears that some atoms get far away from the DNA, inside the box.
> Why
> > > does this happen? Does this make my simulation invalid?
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> > >
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Received on Fri Jun 01 2018 - 18:30:04 PDT
