AMBER Archive (2006)

Subject: AMBER: Parmchk problems (parm99.dat)

From: Prashanth Athri (athriprashanth_at_yahoo.com)
Date: Sun Sep 10 2006 - 19:23:25 CDT

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.
-Prashanth

                 
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