VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Feb 19 2003 - 09:16:52 CST

Paul,

The residue names are determined by what's in your charmm topology
file (the file named with your "topology" command). Search for lines
in this file starting with "RESI" to find a complete list of residue
names that psfgen will recognize. You can then use the psfgen "alias"
command to globally substitute one name for another without having to
modify your pdb file. In your case I believe the command would be
"alias residue ARG+ ARG" since ARG is the residue name in the topology
file.

Cheers,
Justin

On Wed, Feb 19, 2003 at 05:58:36PM +1000, Paul Darwen wrote:
>
> I see that psfgen (and CHARMM and NAMD) have an odd way of
> lettering residues. For example, what the PDB calls HIS
> becomes either HSD or HSE and the positive version HIS+
> becomes HSP.
>
> I have some files with ARG+ and LYS+ residues, and I can't
> seem to find the psfgen (and CHARMM and NAMD) equivalent.
> I'm assuming they have something similar to HIS/HSD/HSE/HSP
>
> I'ved tried ARP and AGP similar variations, but psfgen still
> chokes on these.
>
> Anyone know what psfgen calls ARG+ and LYS+ in the same way
> that it calls HIS+ HSP?
>
> Thanks in advance.
>
> - Paul
> __________________________________________________________________
>
> Dr. Paul Darwen www.protagonist.com.au/darwen
> Protagonist Pty Ltd darwen_at_protagonist.com.au
> 11 Lang Parade Phone: +61-7-3377-0304
> Brisbane 4064 Australia Fax: +61-7-3377-0333
> __________________________________________________________________
> 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys