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)
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 02 2015 - 08:30:04 PST
