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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Received on Mon Nov 02 2015 - 08:30:03 PST
