I am using Amber12
On Mon, Nov 2, 2015 at 9:46 PM, Jason Swails <jason.swails.gmail.com> wrote:
> What version of Amber are you using?
>
>
> On Mon, Nov 2, 2015 at 11:14 AM, Martina Devi <martinadevi2011.gmail.com>
> wrote:
>
> > I opened the xleap of ff12SB.
> >
> > sample=loadpdb sample.pdb
> > loadamberparamsfrcmod.ionsjc_tip3p
> > addions sample Na+ 0
> > saveamberparm sample sample.prmtop sample.inpcrd
> >
> > AMBERHOME/bin/sander -O -i sample.mdin -o sample.mdout -c sample.inpcrd
> -p
> > sample.prmtop -r sample.restrt
> >
> > AMBERHOME/bin/ambpdb -p sample.prmtop < sample.restrt > sample_min.pdb
> >
> > This is how I generated the sample_min.pdb
> >
> > Thankyou
> > Martina
> >
> > On Mon, Nov 2, 2015 at 9:17 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> > > On Mon, Nov 2, 2015 at 6:41 AM, Jason Swails <jason.swails.gmail.com>
> > > wrote:
> > > > tleap does not print anything in the element field (ParmEd and
> cpptraj
> > I
> > > > think both *do* put something here, but I'm not positive about that).
> > >
> > > FYI, cpptraj will print element information to PDB files. If no
> > > element information is available it tries to determine the element
> > > from atom name/mass. If the problem in fact is element info the fix
> > > could be as simple as:
> > >
> > > cpptraj -p input.pdb -y input.pdb -x output.pdb
> > >
> > > -Dan
> > >
> > > >
> > > > Which means if the original PDB came from tleap, then the elements
> must
> > > > have been added "by hand" after-the-fact.
> > > >
> > > > All the best,
> > > > Jason
> > > >
> > > > --
> > > > Jason M. Swails
> > > > BioMaPS,
> > > > Rutgers University
> > > > Postdoctoral Researcher
> > > > _______________________________________________
> > > > 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 307
> > > Salt Lake City, UT 84112-5820
> > > http://home.chpc.utah.edu/~cheatham/
> > > (801) 587-9652
> > > (801) 585-6208 (Fax)
> > >
> > > _______________________________________________
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> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Nov 02 2015 - 09:30:03 PST
