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.
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
Received on Thu Sep 15 2011 - 09:00:04 PDT
