[gmx-users] pdb2gmx : treat CL as C

Justin A. Lemkul jalemkul at vt.edu
Tue Nov 17 16:04:21 CET 2009

Nilesh Dhumal wrote:
> Tsjerk,
> When I open di.pdb (output file) in VMD. I see all CL are repalced by C.
> I can't go to next step. What information do you want more.  I checked the
> format of pdb file again. Its looks dioxin.pdb is ok. After running
> pdb2gmx, the di.pdb output file don't have any CL atom. Hopes you get me
> now

Your original question stated that pdb2gmx was causing your CL atoms to be 
treated as C, leading to lots of speculation (ultimately useless) that the 
format of your .pdb file was wrong.  Thanks to Tsjerk for pointing out the error 
in my evaluation (I had things backwards in my head).  Your input and output 
.pdb files, as well as your topology, indicate that you indeed have chlorine 
atoms.  If VMD has a problem interpreting CL1 as chlorine, that is an entirely 
separate issue, one that is ultimately unrelated to Gromacs.

Has VMD been the problem all along?  If so, it would have been vastly more 
useful to indicate this in your original question to save a lot of time.



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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