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

From: Arun Srikanth <>
Date: Thu, 18 Sep 2014 21:43:17 -0400

Hello jason can you please have a look at the files which I sent and also
suggest any other method for the question which I raised in the previous

Arun Srikanth

On Thu, Sep 18, 2014 at 4:36 PM, Arun Srikanth <> wrote:

> 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 ?
> Thanks
> Arun
> On Thu, Sep 18, 2014 at 3:26 PM, Jason Swails <>
> wrote:
>> 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
>> _______________________________________________
>> AMBER mailing list
AMBER mailing list
Received on Thu Sep 18 2014 - 19:00:03 PDT
Custom Search