Re: [AMBER] Two questions about Net charge and write frcmod in

From: Arun Srikanth <>
Date: Thu, 18 Sep 2014 16:36:34 -0400

I am creating this new bond using vmd by uploading the mol2 file and
created the bond. Saved the new mol2 file. Then I used leap to tell me what
are the parameters for this new topology. I finally used to
print out the bonds, angles and dihedrals.

Then I use the diff and sort command for the files which contain old bonds,
angles and dihedral and the new bond, angles and dihedrals to see what type
of bonds, angles and dihedrals are introduced.

I had to write to script which will then tell me the unique types (bonds,
angles, dihedrals) that are formed.
Is there a neater way ?

Did you have a look at the previous files that I sent ?


On Thu, Sep 18, 2014 at 3:26 PM, Jason Swails <>

> On Thu, 2014-09-18 at 14:32 -0400, Arun Srikanth wrote:
> > Thanks jason.
> > I am attaching the mol2, topology file and the resulting frcmod file
> which
> > I obtained using write frcmod command. Please have a look
> >
> > I have two other questions:
> >
> > 1. I am creating a bond between two atoms. This bond is introducing new
> > angles, dihedrals. I need to know what unique type of new angles and
> > dihedrals this bond introduces in the system.
> How are you creating this new bond?
> > Can this be done using and is there any neater way ?
> You _can_ do this in using the setBond, setAngle, and
> addDihedral commands, but note that adding a bond will _not_ add all of
> the angles and dihedrals that will be formed by the new bond. You have
> to do each of those by hand. And note that the frcmod file may be hard
> to print out if you start changing parameters (since then a bond between
> two of the same atom types can have different values).
> >
> > 2. What is the meaning of the string "M" and "I" that is printed on the
> > left most corner when printdihedrals command is issued in
> An "I" indicates that this is an improper torsion. A "M" indicates that
> the end-group interactions are neglected (i.e., the 1-4 vdW and 1-4
> electrostatic interactions are not calculated for that torsion). This
> occurs in rings with 6 atoms or fewer and for all but one term of a
> multi-term dihedral (I originally chose "M" to indicate "multiterm", but
> it also applies to ring torsions that have only 1 term but whose
> end-groups are excluded by virtue of being 1-3 or 1-4 partners of a
> different group). In retrospect, the "E" printed by rdparm is probably
> a better choice, and will likely be changed in the next version of
> ParmEd (unless there are people that speak up against it).
> HTH,
> Jason
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
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Received on Thu Sep 18 2014 - 14:00:02 PDT
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