Try removing the CONECT cards from the pdb and retrying.
Good luck,
Jason
On Sun, Jan 23, 2011 at 11:35 PM, subrata paul <paul.subrata34.gmail.com>wrote:
> Dear Case
>
> Thank you and sorry for the inconvenience.
>
> I have already gone through this tutorial, and i already tried for my
> compound.When I run with this command ,I got following error.
> antechamber -i dye.pdb -fi pdb -o dye.mol2 -fo mol2 -c bcc -s 2
> 1 is not a valid atom id in CONECT 1 6
>
> How can i solve this?
>
> thanking you
> subrata
> On Sat, Jan 22, 2011 at 6:54 PM, case <case.biomaps.rutgers.edu> wrote:
>
> > On Sat, Jan 22, 2011, subrata paul wrote:
> > >
> > > I want to save prmtop and inpcrd file for a dye. First, I loaded the
> pdb
> > > file for dye.
> > > Then I tried to save the prmtop and inpcrd file but some FATAL error is
> > > coming.
> >
> > Please follow the procedure outlined in Tutorial B4 to set up a
> simulation
> > for
> > a general organic molecule.
> >
> > [Also, think about what someone reading your email would learn about your
> > problem: basically nothing. You tried to run Amber (probably the tleap
> > program) and you encountered some error. You won't get much help from a
> > mailing list without providing *some* level of detail.]
> >
> > ...dac
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Jan 23 2011 - 21:00:06 PST
