VMD-L Mailing List

From: Ioana Cozmuta (ioana_at_nas.nasa.gov)
Date: Thu Jan 16 2003 - 21:05:34 CST

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