Try using cpptraj instead of ambpdb to create the PDB file as Dan suggested.
Also, I suggest upgrading to AmberTools 15.
HTH,
Jason
On Mon, Nov 2, 2015 at 12:24 PM, Martina Devi <martinadevi2011.gmail.com>
wrote:
> 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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> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > > _______________________________________________
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> > > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Mon Nov 02 2015 - 10:00:03 PST
