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.
-Justin
--
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
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
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