Re: [AMBER] Cofactor parametrization

From: Hannes Loeffler <>
Date: Mon, 2 Mar 2015 11:29:31 +0000

You have still not told us exactly how you ran antechamber. What does
sqm.out say? I don't think it matters what Sybyl type you assign
because antechamber will use it's own perception algorithm to do that.
The Sybyl type is on the pyridine N by the way which does not
indicate that it is charged. This doesn't matter anyway because you
only need the total charge for sqm.

Finally, why do you want to parameterise this yourself? You may be
better off looking into the literature or probably the R.E.D.
database. You have a highly charged system there which will tend to
"fold up" i.e. minimised into a conformation that is probably not
relevant for your case. A residue based approach would probably
be better here.


On Mon, 2 Mar 2015 11:08:08 +0000
Francesca Tessaro <> wrote:

> Thank you Jason for your kelp,
> when I am running antechamber the error message that occurs is:
> > Error: cannot run "/usr/local/amber12/bin/sqm -O -i -o
> > sqm.out" of mul() in charge.c properly,
> exit
> I am trying to modify the atom type with sybyl (especially for my
> positive nitrogen in the pyridine ring) and running different command
> with antechamber, always with a net charge of -3 (-nc -3) but it
> still not working.
> If you have any suggestion would be really appreciated,
> I attached also my mol2 file
> Thank you,
> Francesca
> Da: Jason Swails []
> Inviato: giovedì 26 febbraio 2015 17.22
> A:
> Oggetto: Re: [AMBER] Cofactor parametrization
> On Thu, 2015-02-26 at 14:45 +0000, Francesca Tessaro wrote:
> > Hello,
> >
> > I am running MD of a protein with NADP+ as cofactor.
> >
> > I have some troubles with the cofactor parametrization:
> > antechamber is not recognizing the charge of my mol2 file and as
> > well pdb file.
> What error messages are you getting? This description doesn't help us
> figure out what your problem is.
> > So I decided to dowload the prep and frcmod files from Amber
> > parameter database but I don't know how to integrate them with my
> > mol2 or pdb file.
> The prep file defines a residue. It replaces the mol2 file, so all
> you need is the PDB file. You have to make sure that the residue name
> defined in the prep file matches the name assigned to that residue in
> the PDB file. You also need to make sure that the names of the atoms
> defined in the prep file matches the names of the atoms for that
> residue in the PDB file. This is how LEaP knows which atom in the
> residue template (prep or mol2 file) maps to which atom in the PDB
> file.
> Then you need to load the prep and frcmod file in tleap when you
> parametrize your system.
> If you have future questions, please tell us briefly exactly what you
> did (don't describe it, give us actual input and actual output).
> Those are much easier questions to answer, because we don't have to
> guess anything.
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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> AMBER mailing list

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Received on Mon Mar 02 2015 - 03:30:03 PST
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