AMBER Archive (2006)

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

From: Junmei Wang (jwang_at_encysive.com)
Date: Tue Sep 12 2006 - 13:41:21 CDT

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
 
Junmei

From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
Of Prashanth Athri
Sent: Tuesday, September 12, 2006 10:54 AM
To: amber_at_scripps.edu
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 <jwang_at_encysive.com> wrote:

                Please attach the trouble molecules. I tested parmchk
with phenol by using similar commands you used and it works fine.
                 
                All the best
                 
                Junmei
                 
                
                From: owner-amber_at_scripps.edu
[mailto:owner-amber_at_scripps.edu] On Behalf Of Prashanth Athri
                Sent: Sunday, September 10, 2006 7:23 PM
                To: amber_at_scripps.edu
                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.
                        -Prashanth
                        

        


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