Re: [AMBER] parmchk2 issue

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

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?

(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.)

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.


cc-ing Junmei, in case he has ideas here....

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Received on Mon Aug 15 2016 - 09:30:02 PDT
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