Re: Generating psf files for non-proteins

From: Mike McCallum (mmccallum_at_pacific.edu)
Date: Thu Apr 08 2004 - 16:22:43 CDT

Hi Greg,

Here are some links that may help with what you are looking for. I
learned how to generate PSF stuffs using charmm, which may or may not
be easier as it doesn't depend upon scripting. Once you can use psfgen
to reproduce what a tutorial does, you may be able to use the charmm
PSF generation sites to guide you using psfgen.

HTH

(stuff I've generated for my students)
http://onsager.cop.uop.edu/~mccallum/Group/helical_tut/
http://onsager.cop.uop.edu/~mccallum/Group/helical_tut2/
http://onsager.cop.uop.edu/~mccallum/Group/helical_tut3/
http://onsager.cop.uop.edu/~mccallum/Group/namd1/

(NAMD/psfgen site)
http://www.ks.uiuc.edu/Research/namd/tutorial/NCSA2002/hands-on

(charmm PSF tutorials)
http://persweb.wabash.edu/facstaff/fellers/tutorial/butane_tutorial/
http://persweb.wabash.edu/facstaff/fellers/tutorial/water_tutorial/

I personally feel that psfgen is one tool that is extremely powerful to
generate input files for namd (and charmm and...), BUT it is also very
poorly documented and explained, IMHO.

On Apr 8, 2004, at 11:08, Scott, Greg wrote:

> Hi,
>
> I am new to NAMD and was hoping to use it to look at some smaller,
> non-protein systems. I have tried to use psfgen to build a psf file
> from a pdb file that I have generated by using steps similar to those
> posted in the tutorials for converting protein pdb files to psf files,
> but have not had any success. I have also tried to build a psf file
> manually, but have apparently not done that correctly either. Is it
> possible that my pdb file is not in the right format since I don't
> have any residue names? I assume that psfgen should be able to handle
> small systems, but I have been unable to get it to work properly. If
> anyone can point me in the right direction on how to generate psf
> files for small, non-protein molecules, I would greatly appreciate the
> help.
>
> Thank you,
> Greg Scott
>
>
>

--
C. Michael McCallum                        
http://chem.cop.uop.edu/cmmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  / 
(209) 946-2607 fax
--
C. Michael McCallum                        
http://chem.cop.uop.edu/cmmccallum.html
Associate Professor
Department of Chemistry, UOP
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  / 
(209) 946-2607 fax

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