VMD-L Mailing List
From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Tue Dec 02 2014 - 03:58:11 CST
First obtain a mol2 file of your molecule. I think you can draw the
molecule with avogadro <http://avogadro.cc/wiki/Main_Page>.
Then upload the mol2 file into paramchem <https://cgenff.paramchem.org/>.
This will give you a param and psf file. Then use the forcefield toolkit to
optimize the parameters with large errors.
On 2 December 2014 at 09:56, Kshatresh Dutta Dubey <kshatresh_at_gmail.com>
> Dear Users,
> I am trying to parameterise on non-standard residues using forcefield
> toolkit in vmd, however I am unable to get the corresponding psf and
> parameter file of that non-standard residue which are pre-requisite of
> forcefield toolkit. I wonder that how I can get the psf and parameter files
> before the parameterisation.
> I will be thankful if someone can suggest me in this context.
> With Regards
> Kshatresh Dutta Dubey