Thank you Dr. Cuebas
On Fri, Sep 16, 2011 at 3:38 AM, Dean Cuebas
<deancuebas.missouristate.edu>wrote:
> 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
> >_______________________________________________
> >AMBER mailing list
> >AMBER.ambermd.org
> >http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Chidambar k
Int.PhD
JNCASR
Bangalore
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Received on Thu Sep 15 2011 - 23:00:03 PDT
