Re: [AMBER] parmchk2 issue

From: Hannes Loeffler <>
Date: Tue, 16 Aug 2016 09:35:08 +0100

On Mon, 15 Aug 2016 12:06:35 -0400
David A Case <> wrote:

> On Mon, Aug 15, 2016, Hannes Loeffler wrote:
> >
> > I have a problem with parmchk2 (but not with parmchk) and a mol2
> > file of mine (see attachment, types zz and du are defined in my,
> > modified PARMCHK.DAT). The command
> >
> > # parmchk2 -i MORPH.mol2 -f mol2 -o MORPH.frcmod -a N -p
> > $AMBERHOME/dat/leap/parm/GLYCAM_06j.dat
> >
> > comes back with
> >
> > Atom type of Ho does not shown up in PARMCHK.DAT
> I'm not sure how you modified PARMCHK.DAT, but the description above
> suggests that this message is correct: "Ho does not show up in
> PARMCHK.DAT." Is that correct?

Yes, Ho is not in PARMCHK.DAT but in
$AMBERHOME/dat/leap/parm/GLYCAM_06j.dat. I would expect to be able to
tell parmchk2 that it should not bother with some types that are in
some other database it can read. I thought this is what the -p switch
is for and this seems to work with parmchk, and parmchk2 in amber12 (not
sure what exact version I have here). Something has changed since
then and this looks like a bug to me.

> (parmchk2 is intended to be used to do interpolations/extrapolations
> to estimate parameters that are not in the input parm.dat files; it
> can only do this is the proper information is provided in the
> PARMCHK.DAT file. And the PARMCHK.DAT file in
> $AMBERHOME/dat/antechamber does not know about GLYCAM atom types.)
> You might try the "-pf 2" flag here (not sure what that does, myself.)

Doesn't make any difference.

> The other alternative is to use tleap to create a prmtop file from
> MORPH.mol2, then use parmed to create the frcmod file from that
> prmtop. I guess I'm not sure what you plan to do with the
> MORPH.frcmod file once it is generated.

That won't work in this case because I have those dummy types. I
expect parmchk2 to create the respective force field entries for me
(even though they are all zero).


AMBER mailing list
Received on Tue Aug 16 2016 - 02:00:02 PDT
Custom Search