Fantastic! Thank you very much
On Fri, Nov 22, 2013 at 2:54 PM, Brian Radak <radak004.umn.edu> wrote:
> P.S. You can use babel to convert pdbs to xyz format. It should be
> available in the repositories of most Linux distributions.
>
> example:
> babel -ipdb <pdbfilename> -oxyz <xyzfilename>
>
>
> On Fri, Nov 22, 2013 at 2:41 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > No, there is not a standard tool for doing this. However, I cobbled
> > together a Python script for doing it a while back (attached, no
> > warranty!). It is somewhat robust and flexible, but was really made to
> fit
> > my purpose at the time. If there is interest I might clean it up and put
> it
> > in AmberTools.
> >
> > Regards,
> > Brian
> >
> >
> >
> > On Fri, Nov 22, 2013 at 1:48 PM, Geoffrey Gray <gmgray2.mail.usf.edu
> >wrote:
> >
> >> I am trying to run a single-point energy calculation using sqm in
> >> AmberTools13. Is there an easy way to convert to the required file
> format
> >> shown in the documentation (ex. page 199) when starting from a pdb?
> >> Thanks,
> >>
> >> Geoffrey
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> >
> >
> >
> > --
> > ================================ 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.
> >
>
>
>
> --
> ================================ 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
>
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Received on Sat Nov 23 2013 - 07:30:02 PST
