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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>> 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.
>
--
================================ 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 Fri Nov 22 2013 - 12:00:06 PST
