AMBER Archive (2006)

Subject: RE: AMBER: Parmchk problems (parm99.dat)

From: Junmei Wang (
Date: Mon Sep 11 2006 - 15:48:51 CDT

Please attach the trouble molecules. I tested parmchk with phenol by
using similar commands you used and it works fine.
All the best

From: [] On Behalf
Of Prashanth Athri
Sent: Sunday, September 10, 2006 7:23 PM
Subject: AMBER: Parmchk problems (parm99.dat)

        Dear users:
        [I have tried to use the most updated antechamber as suggested
by previous threads....this gives the same problem.]
        When I run use
        "antechamber -at amber ......"
        the output has amber atomtypes (as expected)
        Now, when I run
        "parmchk -p $AMBERHOME/dat/leap/parm/parm99.dat -i
antechamber_output.mol2 -f mol2 -o missing parm.frcmod"
        The output does not reflect the parameters that are present in
parm99.dat. Instead most parameters are shown to be missing(all values
are zerous, i.e the ff params). Is there anything obviously wrong in
what I am doing?
        I am trying to some dihedral calculations on benzimidazole-
phenyl system. This problem is with respect to the benzimidazole, which
has a five membered ring very similar to the Ade, Gua systems, hence the
use of parm99.dat
        Ofcourse I can manually change every value, does anyone have
other suggestions? Thx in advance.

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