RE: AMBER: Parmchk problems (parm99.dat)

From: Prashanth Athri <>
Date: Tue, 12 Sep 2006 08:54:08 -0700 (PDT)

Thanks for the reply-- here are the files.
I have attached a copy of the parm99.dat file that I use as well.

In the .frcmod file, there are a lot of parameters that are already parameterized in the parm99.dat file. (using Amber 8)

Junmei Wang <> wrote:Message 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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Received on Wed Sep 13 2006 - 06:07:14 PDT
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