VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Thu Jan 16 2003 - 23:26:37 CST

Hi,

I'm forwarding your question to the NAMD mailing list. Jim, our main
NAMD developer, may have an answer for you. Jim, please CC vmd-l in
your response.

Cheers,
Justin

On Thu, Jan 16, 2003 at 07:05:34PM -0800, Ioana Cozmuta wrote:
> Hi,
>
> I have a structure that contains 7 Cl- counterions. I am trying to
> generate the psf file in vmd/psfgen and I use the topology file from
> http://www.chpc.utah.edu/~cheatham/software.html
> cornell_all.rtf.
>
> My initial pdb file is generated from the .prmtop and .prmcrd files from
> amber so the name of the Cl ions is Cl-. When I load the above topology
> file and try to generate a segment from the pdb file I get an error
> message saying
> unknown residue type Cl-
> Info: generating structure...
> unknown residue type Cl-
> ERROR: failed on end of segment
>
> The name of the atom in the rtf file is IM and the residue associated to
> it is
>
> RESI Cl -1.00 ! Chloride Ion
> GROUP
> ATOM Cl IM -1.00
> PATCHING FIRST NONE LAST NONE
>
> In my pdb file I have
> ATOM 32306 Cl- Cl- 2052 44.691 48.253 10.626 -1.0000 1.700
>
> So after loading the topology file I did alias the residue name first then
> the atom
>
> alias residue Cl- Cl
> alias atom Cl Cl- C
>
> However I keep on getting the same error.
> Could you please help?
>
> THank you,
> Ioana 

-- 
  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