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

From: Jason Swails <jason.swails.gmail.com>
Date: Fri, 19 Sep 2014 08:12:45 -0400

On Thu, Sep 18, 2014 at 11:50 PM, Arun Srikanth <askforarun.gmail.com>
wrote:

> 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 paramed.py 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.
>

‚ÄčThe only parameters that could have been duplicated in the frcmod file was
the bond parameters. As long as you use the latest version of ParmEd, this
should be fixed and there will be no need to filter redundant types.

Other than this last part, this is exactly what I would do.

HTH,
Jason‚Äč

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Sep 19 2014 - 05:30:02 PDT
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