From: Christopher Harrison (char_at_ks.uiuc.edu)
Date: Sat Oct 13 2007 - 14:55:34 CDT
oops . . . just a quick note . . . we're using the term "forcefield"
here but we're really talking about which topology files are used
during psf generation. The "forcefield" is composed of a combination
of items including the topology, parameters (which are in the par*
files called by NAMD's "parameters" command), and the functional form
used (which is hard-coded into NAMD).
Chris
On Oct 13, 2007, at 2:43 PM, Christopher Harrison wrote:
> 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.
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