Use the -a Y option with parmchk to print out all force field parameters.
Hope this helps,
Dean--
Dr. Dean Cuebas, Associate Prof of Chemistry
deancuebas.missouristate.edu, Ph 417-836-8567 FAX 417-836-5507
Dept. of Chemistry, Missouri State University
Springfield, Missouri 65897
On 9/15/11 12:07 PM, "Jason Swails" <jason.swails.gmail.com> wrote:
>On Thu, Sep 15, 2011 at 11:42 AM, Chidambar Kulkarni
><chidkul007.gmail.com>wrote:
>
>> Thanks Jason for the valuable suggestions.
>> But I have another question; In my frcmod file, I can only see the
>>missing
>> dihedrals ( 4 dihedrals). So how to modify the other dihedrals. I am
>>also
>> attaching the frcmod file here (below is the .frcmod file). Thanks a
>>lot.
>>
>
>Just put them in in the same format as they exist in your frcmod file.
>They
>will overwrite the ones loaded in the existing force field as long as you
>load your frcmod after the force field data file.
>
>
>>
>> remark goes here
>> MASS
>>
>> BOND
>>
>> ANGLE
>>
>> DIHE
>>
>> IMPROPER
>> c -ca-ca-ca 1.1 180.0 2.0 Using
>>default
>> value
>> ca-ca-ca-ha 1.1 180.0 2.0 General
>> improper
>> torsional angle (2 general atom types)
>> ca-n -c -o 10.5 180.0 2.0 General
>> improper
>> torsional angle (2 general atom types)
>> c -hn-n -hn 1.1 180.0 2.0 General
>> improper
>> torsional angle (2 general atom types)
>>
>> NONBON
>>
>>
>> On Thu, Sep 15, 2011 at 8:09 PM, Jason Swails <jason.swails.gmail.com
>> >wrote:
>>
>> > I would urge against changing the dihedral parameter in the topology
>>file
>> > itself. Instead, change the parameter in an frcmod that you load into
>> > leap. The topology file is not really meant to be human-readable (you
>> also
>> > have to take care that the units are what you're expecting -- leap
>>makes
>> a
>> > number of unit conversions before writing the topology file for
>>runtime
>> > efficiency in sander and pmemd).
>> >
>> > The prmtop format is specified here: http://ambermd.org/formats.html,
>> but
>> > it
>> > takes a good deal of time studying the format (and the code) in order
>>to
>> > get
>> > a good grasp of what it means.
>> >
>> > HTH,
>> > Jason
>> >
>> > On Thu, Sep 15, 2011 at 10:14 AM, Chidambar Kulkarni
>> > <chidkul007.gmail.com>wrote:
>> >
>> > > Dear Amber users,
>> > > I am trying to set up an organic molecule
>> using
>> > > antechamber and tleap. I want to change the parameters for a
>>dihedral
>> > angle
>> > > generated from tleap ( in the .prmtop file). But I am unable to make
>> out
>> > > which parameters correspond to which dihedral angle. Can anyone help
>> me.
>> > >
>> > >
>> > > Thanks in advance.
>> > > --
>> > > Chidambar k
>> > > Int.PhD
>> > > JNCASR
>> > > Bangalore
>> > > _______________________________________________
>> > > AMBER mailing list
>> > > AMBER.ambermd.org
>> > > http://lists.ambermd.org/mailman/listinfo/amber
>> > >
>> >
>> >
>> >
>> > --
>> > Jason M. Swails
>> > Quantum Theory Project,
>> > University of Florida
>> > Ph.D. Candidate
>> > 352-392-4032
>> > _______________________________________________
>> > AMBER mailing list
>> > AMBER.ambermd.org
>> > http://lists.ambermd.org/mailman/listinfo/amber
>> >
>>
>>
>>
>> --
>> Chidambar k
>> Int.PhD
>> JNCASR
>> Bangalore
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
>--
>Jason M. Swails
>Quantum Theory Project,
>University of Florida
>Ph.D. Candidate
>352-392-4032
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>AMBER mailing list
>AMBER.ambermd.org
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Received on Thu Sep 15 2011 - 15:30:02 PDT
