From: David Hardy (dhardy_at_ks.uiuc.edu)
Date: Tue Jul 24 2012 - 12:19:41 CDT

Hi Ganesh,

Although psfgen does not yet support the Drude model, I think that it would not be too hard to make a script that generates a Drude water PSF. Also, it should not be hard to convert a TIP3 PDB file to Drude SWM4.

There is a small system of Drude SWM4 water that you can download from http://www.ks.uiuc.edu/Research/Drude/ to use as a guide.

You have to add the "DRUDE" keyword to the top line. You'll have to change the atom section to 5 particles, rather than 3, with the extra columns as shown. For the bond part, you will have to add bonds from oxygen to Drude and oxygen to LP. Nothing needs to be added to the angle section, just renumbering the atoms. Looks like you'd have to change acceptors, NNB, NGRP sections to accommodate the new number of atoms, although I don't remember NAMD doing anything with NGRP. You might also be able to omit MOLNT section. The NUMLP section is required, as it gives constants and geometries for the lone pair particle for each water, but you should be able to extend the example shown for whatever size system you have.

Hope this helps,
Dave

On Jul 24, 2012, at 11:36 AM, John Stone wrote:

> Hi,
> I asked my colleague David Hardy about this, as he has been
> the main force in adding support for Drude to NAMD. David
> indicated that psfgen has not yet been updated to support
> Drude, but that he can give you some alternatives that would
> likely help you get up and running. I've CCed David on this
> email so that you can discuss further.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Tue, Jul 24, 2012 at 11:19:03AM -0500, Ganesh Kamath wrote:
>> Hi Folks,
>>
>> Can we generate the psf for Drude polarizable water model using psfgen
>> in vmd?
>>
>> thanks,
>> ganesh
>
> --
> NIH Resource for Macromolecular Modeling and Bioinformatics
> Beckman Institute for Advanced Science and Technology
> University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
> http://www.ks.uiuc.edu/Research/vmd/ Fax: 217-244-6078

--
David J. Hardy, Ph.D.
Theoretical and Computational Biophysics
Beckman Institute, University of Illinois
dhardy_at_ks.uiuc.edu
http://www.ks.uiuc.edu/~dhardy/