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
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
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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