[gmx-users] CL atom not being recognised

Justin A. Lemkul jalemkul at vt.edu
Tue Jun 29 01:15:40 CEST 2010

jayant james wrote:
> Hi!
> The protein I am attempting to simulate has a CL atom. When I run 
> pdb2gmx I get the following error message. Any help in overcoming this 
> problem would be appreciated.
> Thanks
> James 
> ------------------------------------------------------
> Program pdb2gmx, VERSION 4.0
> Source code file: pdb2gmx.c, line: 429
> Fatal error:
> Atom CL- in residue CL- 574 not found in rtp entry with 1 atoms
>              while sorting atoms
> -------------------------------------------------------

You haven't told us which force field you're trying to use, but I'm guessing 
that the chloride .rtp entry is probably named "CL" instead of "CL-" (which is 
used by the ffG* force fields).  You can check the .rtp file to be sure.

Also, I would strongly suggest upgrading to version 4.0.7 - there have been 
numerous bug fixes and performance upgrades since version 4.0.


> -- 
> Jayasundar Jayant James
> www.chick.com/reading/tracts/0096/0096_01.asp 
> <http://www.chick.com/reading/tracts/0096/0096_01.asp>)


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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