AMBER Archive (2009)

Subject: Re: [AMBER] antechamber : missed atoms

From: Khaled Barakat (kbarakat_at_phys.ualberta.ca)
Date: Mon Jan 26 2009 - 14:22:14 CST

Attached is the mol2 file, it has all atoms

> Have you tried outputting using the mol2 file format?
>
> -sean
>
> Sean Johnston
> johnstos_at_stolaf.edu
> sean.johnst_at_gmail.com
>
> On Mon, Jan 26, 2009 at 1:20 PM, Khaled Barakat
> <kbarakat_at_phys.ualberta.ca>wrote:
>
> > Sorry I forgot to attache files !
> >
> > > Hello,
> > >
> > > I am trying to use Antechamber from Ambertools 1.2 to get parameters for
> > a set of ligands. The
> > > input pdb files for antechamber seem to be OK . Attached is an example of
> > these ligands along
> > with
> > > the NEWPDB.PDB generated by Antechamber. As you can see there are some
> > missing atoms in the
> > > NEWPDB.PDB file.
> > >
> > > I am using the command:
> > > antechamber -i ref.pdb -fi pdb -o ref.prepin -fo prepi -rn UNK -s 2 -at
> > gaff
> > >
> > > and of course when I run the command
> > > parmchk -i ref.prepin -f prepi -o ref.frcmod
> > >
> > > I get Bus error.
> > >
> > > I am wondering if some one can help me to solve this problem and preserve
> > these atoms?
> > >
> > > with my best regards
> > >
> > > khaled
> > >
> > > _______________________________________________
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> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> >
> >
> >
> >
> >
> >
> >
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  • application/octet-stream attachment: ref.mol2

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