Sorry, I have wind in my head,
I use another computer for calculations, just checked:
I used:
prot = loadpdb prot.pqr
It gives huge number of warnings and mistakes
And finally, downloaded structure is not possible to use
On Thu, Jun 9, 2011 at 3:10 PM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> 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!
> > >>> > _______________________________________________
> > >>> > AMBER mailing list
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> > >>> > http://lists.ambermd.org/mailman/listinfo/amber
> > >>> >
> > >>>
> > >>>
> > >>>
> > >>> --
> > >>> Dr. Daniel J. Sindhikara
> > >>> Institute for Molecular Science
> > >>> E-mail: sindhikara.gmail.com
> > >>> Website: http://sites.google.com/site/dansindhikara/
> > >>> --
> > >>> _______________________________________________
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> > >>> AMBER.ambermd.org
> > >>> http://lists.ambermd.org/mailman/listinfo/amber
> > >>>
> > >>
> > >>
> > >>
> > >
> > _______________________________________________
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> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Dr. Daniel J. Sindhikara
> Institute for Molecular Science
> E-mail: sindhikara.gmail.com
> Website: http://sites.google.com/site/dansindhikara/
> --
> _______________________________________________
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>
--
Best regards,
Azat Mukhametov, PhD
Centre for Chemical Biology at Universiti Sains Malaysia (CCB.USM)
1st Floor, Block B,
No.10, Persiaran Bukit Jambul,
11900 Bayan Lepas,
Penang, Malaysia.
http://www.ccbusm.com
Tel : +604-6535500/5573
Fax : +604-6535514
email: azatccb.gmail.com
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Received on Thu Jun 09 2011 - 00:30:03 PDT
