VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Mon Nov 04 2013 - 16:35:20 CST

Hi Ramin,

One of the easiest ways I've gotten parameter and topology files in the
past was to build the molecule in Avogadro (or anything else that spits
out a mol2 file with the connection information you want), and then
submit the mol2 file to paramchem. First though, I'd look through the
"Parameterizing a Novel Residue" tutorial
(http://www.ks.uiuc.edu/Training/Tutorials/spectop-index.html#novelresidue).
It lays out some of the basics with respect to what a parameter and
topology file look like, and how you can write your own (or check the
validity of what paramchem gives you). You can feel free to ignore the
parameterization part of the tutorial, as that has been replaced by FFTK
(http://www.ks.uiuc.edu/Research/vmd/plugins/fftk/), and the tutorial
hasn't been updated yet.

-Josh Vermaas

On 11/04/2013 01:51 PM, Ramin Ekhteiari wrote:
> Hi,
>
> I want to simulate a protein that include a compound like this (C34
> H32 Fe N4 O4), so can someone advise me on how to generate parameter
> and topology file for this compound, to use at namd.
>
> Would be grateful for any advice,
>
> Cheers,
> Ramin
> _