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

From: Arun Srikanth <>
Date: Thu, 18 Sep 2014 23:50:41 -0400

The following questios is for amber users. Sorry for the mix up btween
lammps and amber users. I want your suggestion on the following method of
computing new angles and dihedral type the bond introduces or can u suggest
a shorter way ?

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 which I can directly obtain the bond types and angle
types and dihedral types that are formed.


On Thu, Sep 18, 2014 at 11:41 PM, Arun Srikanth <>

> Thank u very much jason
> On Thu, Sep 18, 2014 at 10:27 PM, Jason Swails <>
> wrote:
>> On Thu, Sep 18, 2014 at 9:43 PM, Arun Srikanth <>
>> wrote:
>> > 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
>> > post
>> >
>> ​It actually only ever printed duplicate bond types, so the angles and
>> dihedrals should all be unique (note that there may be multiterm dihedrals
>> so that the same 4 atoms are defined multiple times, but each is a
>> separate
>> term in the Fourier expansion for that torsion). I've found the problem
>> and fixed it. I should hopefully be able to post an update for this in a
>> couple days.
>> If, as your recent emails suggest, your need for this is too urgent to
>> wait
>> for that, you can access the current development version of ParmEd on
>> Github ( -- note the release versions
>> posted there do not have the fix, only the latest git version does.
>> ​Thanks for the report,
>> Jason​
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>> _______________________________________________
>> AMBER mailing list
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Received on Thu Sep 18 2014 - 21:00:03 PDT
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