Good point.
I am using AmberTools12. Apparently it may be an old version.
I just thought it worthed mentioning. It took me a while to find the error
in my files.
2014-03-26 16:16 GMT+01:00 Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> What version of AmberTools are you using, and what patches have been
> applied?
>
> -Dan
>
>
> On Wed, Mar 26, 2014 at 9:10 AM, Ilias Patmanidis <
> patmanidis.ilias.gmail.com> wrote:
>
> > Dear AMBER users,
> >
> > I was using xleap to generate topology and coordinate files for a
> specific
> > system
> >
> > >source leaprc.ff12SB
> > >loadamberparams frcmod.ionsjc_tip3p
> > >test = loadPDB test.pdb
> > >addions test Na+ 2
> > >solvatebox test TIP3PBOX 10
> > >savePDB test test1.pdb
> > >saveamberparm test test.prmtop test.crd
> >
> > Information about the vdw box size was missing from the end of the
> > generated test.crd.
> >
> > This problem did not appear in tleap. The same commands gave a different
> > output with the vdw box size included in the end of the file.
> >
> > Best regards,
> > Ilias Patmanidis
> >
> > --
> > Ilias Patmanidis
> > University of Geneva, Switzerland
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ilias Patmanidis
MSc student in Bioinformatics and data analysis in biology,
University of Geneva, Switzerland
Tel(mob):
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Received on Wed Mar 26 2014 - 09:00:02 PDT
