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.
....dac
cc-ing Junmei, in case he has ideas here....
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 15 2016 - 09:30:02 PDT
