Not sure how many folks here use parmchk2, but it won't hurt to make them
think about it.
Here's the GLYCAM mailing list:
https://listserv.uga.edu/cgi-bin/wa?A0=GLYCAM-L
There are more folks who know the force field that monitor that list than
this one.
On Mon, Nov 28, 2016 at 2:57 PM, David A Case <david.case.rutgers.edu>
wrote:
> On Fri, Nov 25, 2016, Sonia Romero wrote:
> >
> > parmchk2 -i UGN_mod_leap.mol2 -f mol2 -o UGN_mod_leap.frcmod -p
> > $AMBERHOME/dat/leap/parm/GLYCAM_06j.dat
> >
> > the result was
> >
> > Atom type of Cg does not shown up in PARMCHK.DAT
>
> The parmchk2 program relies on a "similarity index" (contained in the
> PARMCHK.DAT file) that defines connections between GAFF and standard Amber
> parameters. Unfortunately, it does not know anything about Glycam atom
> types,
> and so gives the message above. You will have to establish a connection
> between gaff and Glycam atom types by hand.
>
> [The documentation is certainly unclear about this: we will get this
> updated
> for the next release.]
>
> Alternatvie to is ask at the glycam web site, and see what they recommend
> for
> doing what you want to do.
>
> ....dac
>
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Tue Nov 29 2016 - 00:00:03 PST
