Re: Converting a PSF file from one forcefield top another

From: Christopher Harrison (char_at_ks.uiuc.edu)
Date: Sat Oct 13 2007 - 14:43:35 CDT

Hi Illya,

The easiest way may depend on how you generated the initial psf file:

1. If you used a psfgen script with the command line version of
psfgen then you can just change the topology files read at the
beginning of the script so they correspond to the forcefield you
desire and rerun psfgen. (I am assuming when you say different
forcefield you mean another version of the charmm forcefield.
Switching to amber, opls, etc forcefields is a different can of worms.)

2. If you used the Auto-Psf-builder plugin in VMD, I believe you
should be able to just load your old psf and pdb then rerun Auto-
Psf. (In the Tkcon window: "mol new your-psf-file.psf" and "mol
addfile your-pdb-file.pdb".) Then start the Automatic Psf generation
by clicking Extensions -> Modeling -> Automatic PSF Builder. When the
Auto-Psf-builder window opens you'll need to change from the default
forcefield listed to a file(s) containing the forcefield you wish to
use. You can control segname definitions in "Step 3: Chains" of the
Auto-Psf-builder. Then proceed as normal.

Of course, there may be an easy way of which I'm unaware.

Hope this helps get you started.

Chris

On Oct 13, 2007, at 1:14 PM, Ilya Chorny wrote:

> I have a psf file which contains Lipid, water, and trimer protein.
> I want to convert it to a different forcefield. It there any simple
> way to do that? I tried separating monomers, lipid, water, and
> sodium but I get psfgen errors when I include the lipid, water, and
> sodium. My water and lipid are further broken down into multiple
> segments. Will I have to parse each segment?
>
> Thanks,
>
> Ilya
>
> --
> Ilya Chorny Ph.D.

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 15:47:07 CST