RE: AMBER: Parmchk problems (parm99.dat)

From: Junmei Wang <jwang.encysive.com>
Date: Tue, 12 Sep 2006 15:44:30 -0500

Hi, Prashanth,
Amber force fields (parm94, parm99 etc) are mainly for proteins and
nucleic acids and not for small organic molecules. Unlike gaff, which is
a complete force field for the basic atom types, amber force field (such
as parm99) does not have sufficient parameters for most organic
molecules. It is acceptable to borrow parameters from gaff even you
assign amber atom types to your organic molecules since gaff is
parameterized with the similar protocol to that of amber (same function
form, same charge method etc). Please also check the output of the
parmchk I produced for your molecule. There is no "need revision" lines
at all.
 
All the best
 
Junmei
 
From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf
Of Prashanth Athri
Sent: Tuesday, September 12, 2006 2:30 PM
To: amber.scripps.edu
Subject: RE: AMBER: Parmchk problems (parm99.dat)



        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)
        
        Regards,
        Prashanth
        
        
        Junmei Wang <jwang.encysive.com> wrote:

                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.scripps.edu
[mailto:owner-amber.scripps.edu] On Behalf Of Prashanth Athri
                Sent: Tuesday, September 12, 2006 10:54 AM
                To: amber.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.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.scripps.edu
[mailto:owner-amber.scripps.edu] On Behalf Of Prashanth Athri
                                Sent: Sunday, September 10, 2006 7:23 PM
                                To: amber.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
                                


                        


        
________________________________

        Get your email and more, right on the new Yahoo.com
<http://us.rd.yahoo.com/evt=42973/*http://www.yahoo.com/preview>




-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu

Received on Wed Sep 13 2006 - 06:07:18 PDT
Custom Search