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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Received on Thu Sep 15 2011 - 10:30:04 PDT
