AMBER Archive (2009)

Subject: Re: [AMBER] antechamber : missed atoms

From: Sean Johnston (sean.johnst_at_gmail.com)
Date: Mon Jan 26 2009 - 13:40:59 CST

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
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER_at_ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber