You should read the ambertools manual regarding the syntax of the loadpdb
command. You should probably write something like
prot = loadpdb prot.pqr
On Thu, Jun 9, 2011 at 3:57 PM, Azat Mukhametov <azatccb.gmail.com> wrote:
> Oh, sorry, please read:
> loadpdb prot prot.pqr
>
> On Thu, Jun 9, 2011 at 2:56 PM, Azat Mukhametov <azatccb.gmail.com> wrote:
>
> > By the way, it looks that loadpdb has problems with understanding of pqr
> > files, when someone uses a command:
> > loadpqr prot prot.pqr
> >
> > May somebody knows the more reliable way to read pqr into xleap/tleap?
> >
> > Thanks!
> >
> > On Thu, Jun 9, 2011 at 10:57 AM, Azat Mukhametov <azatccb.gmail.com
> >wrote:
> >
> >> OK, thanks much!
> >>
> >>
> >> On Thu, Jun 9, 2011 at 10:50 AM, Daniel Sindhikara <
> sindhikara.gmail.com>wrote:
> >>
> >>> There is a very similar command to "loadpdb" it is called "loadpdb" :)
> >>> I don't think it reads in the charges from the pqr, but it should have
> >>> the
> >>> correct atom naming so that when you load the same parm set that you
> put
> >>> in
> >>> for pdb2pqr it should have the same charges.
> >>> Give it a try!
> >>>
> >>> -Dan
> >>>
> >>>
> >>> On Thu, Jun 9, 2011 at 11:35 AM, Azat Mukhametov <azatccb.gmail.com>
> >>> wrote:
> >>>
> >>> > Hi All,
> >>> > Does anybody know, is it possible to use PQR file produced by PDB2PQR
> >>> to
> >>> > prepare structures for MD simulation?
> >>> > Is here any command like "loadpdb", but for PQR file?
> >>> > Or any other way to perform conversion?
> >>> >
> >>> > Thanks!
> >>> > _______________________________________________
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> >>> >
> >>>
> >>>
> >>>
> >>> --
> >>> Dr. Daniel J. Sindhikara
> >>> Institute for Molecular Science
> >>> E-mail: sindhikara.gmail.com
> >>> Website: http://sites.google.com/site/dansindhikara/
> >>> --
> >>> _______________________________________________
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> >>> http://lists.ambermd.org/mailman/listinfo/amber
> >>>
> >>
> >>
> >>
> >
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--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Thu Jun 09 2011 - 00:30:02 PDT
