AMBER Archive (2006)

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

From: Prashanth Athri (
Date: Tue Sep 12 2006 - 14:30:02 CDT

Dear jumei:
[Sorry about the complications and I do appreciate your taking the time to answer]

I still have some questions about this .
When I use the combined .dat file, I do get lesser "need revision" parameters. Nevertheless, I dont see why that is happening. My ante_output.mol2 file has all parmm99.dat atom types (i.e. all uppercase); and so all parameters should be read in from parm99.dat and not from gaff.dat. The inclusion of gaff.dat should not matter because I am asking it to get it from parm99.dat. Obvuously I am missing somethihg here.
I specifically dont want anything read from gaff.dat-- I just want the parm99.dat parameterization for the assigned atom types (all uppercase)


Junmei Wang <> wrote:Message If one assigns AMBER atom types (in uppercase) and wants to borrow parameters from gaff (all atom types in lowercase), one needs to combine amber protein/nucleic acid force field with gaff for parmchk work properly. Here I attached the combined parm99/gaff parameter file with this email. Since I placed amber parameters before the gaff parameters for each section (element, bond length, bond angle, torsional angle, improper torsional angle, vdw). Amber force field parameters are first considered by parmchk to assign substitutes for the missing parameters.
 Now one can run the following command to get additional force field parameter file
 parmchk -i input.mol2 -f mol2 -o missing_parm.frcmod -p parm_for_parmchk.dat
 All the best

 From: [] On Behalf Of Prashanth Athri
Sent: Tuesday, September 12, 2006 10:54 AM
Subject: RE: AMBER: Parmchk problems (parm99.dat)

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

Junmei Wang <> wrote: 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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