This is probably a VMD "error". The ".crd" file extension is recognized as
an older format (which no part of AMBER uses anymore as far as I can tell)
and VMD does not automatically determine if box info is present or not (*
i.e.* you have to tell it, since I don't think there is an easy way to
discover it on the fly).
My recommendation is to name all AMBER structure files with the extension
".rst7", as VMD will read this correctly provided you are using a recent
version of AMBER.
Regards,
Brian
On Tue, Mar 19, 2013 at 10:48 AM, Albert <mailmd2011.gmail.com> wrote:
> Hello Kshatresh:
>
> thanks a lot for kind reply.
> It still doesn't work even I take your advices.
>
> However, if I use command:
>
> ptraj sys.prmtop ptrja.in
>
> --ptrja.in-----
> trajin npt2.trj 4742
> trajout npt2.crd parm
> -------------
>
> extract information from trajectory, and load npt.crd and sys.prmtop
> into VMD, then it works fine. I don't know why the PBC doesn't work when
> I load the .rst7 file into vmd....
>
>
> best
> Albert
>
>
> On 03/19/2013 03:21 PM, Kshatresh Dutta Dubey wrote:
> > Hi.
> >
> > Use following if you are not doing this in vmd
> >
> > open tk console of vmd and type
> >
> > *package require pbctools*
> > *pbc box*
> >
> > it will work
> >
> > Regards
> > Kshatresh
>
> _______________________________________________
> 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 Tue Mar 19 2013 - 10:30:02 PDT
