Hi,
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
which I assume means that it did not find this particular GLYCAM type.
The file MORPH.frcmod is created but empty. I would expect parmchk2 to
extract information from the file supplied with -p.
Cheers,
Hannes.
Content-Transfer-Encoding: base64
Content-Disposition: attachment; filename=MORPH.mol2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_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Aug 15 2016 - 08:30:03 PDT
