Hello,
I think it's simpler than this, even. tleap has a savepdb function (see
page 60 in the AmberTools 1.4 manual). Using this, all you need is the
amber prep file (not even the frcmod).
Use these commands in leap to write the pdb:
loadamberprep example.prep
savepdb ___ example.pdb
Fill in the blank with the residue name in your amber prep file. Use "list"
to see the name of everything loaded into leap.
Hope this helps,
Jason
On Sat, Jul 31, 2010 at 3:56 PM, Alessandro Nascimento <
al.s.nascimento.gmail.com> wrote:
> There should be an easier way, but what I would do is:
>
> load the prepin/frcmod in leap (using the same ff as before):
>
> If its a small molecule (i.e., using gaff):
>
> cat > leaprc << EOF
> source leaprc.gaff
> loadamberprep file.prein
> loadamberparams file.frcmod
> list // here
> look for your molecule name listed in leap. Assuming <0>
> saveamberparm <0> file.prmtop file.inpcrd
> quit
> EOF
>
> then load the prmtop/inpcrd files in ambpdb:
>
> ambpdb -p file.prmtop <file.inpcrd> file.pdb
>
>
> Hope that helps!!!
>
>
> --Alessandro
>
> On Sat, Jul 31, 2010 at 4:42 PM, Ehsan Habibi <EHabibi.ibb.ut.ac.ir>
> wrote:
> > Hi Amber users,
> > Can we obtain a .pdb file from a .prepin/.frcmod file in Amber? if yes,
> > what's the command line?
> >
> > Regards,
> > Ehsan
> > _______________________________________________
> > 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
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sat Jul 31 2010 - 14:00:02 PDT
