Re: [AMBER] GlcNAc-UDP problem with frcmod file

From: David A Case <>
Date: Mon, 28 Nov 2016 14:57:23 -0500

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.


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Received on Mon Nov 28 2016 - 12:00:04 PST
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