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

From: Jason Swails <>
Date: Thu, 18 Sep 2014 15:26:58 -0400

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).


Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Thu Sep 18 2014 - 12:30:05 PDT
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