Homa Azizian wrote:
Hi
according to my problem about non-neglible magnitude partial charge on
protein, I did not use -missing option with pdb2gmx my command is:
pdb2gmx -ignh -f .pdb -o .pdb -water spce
what should I do to neutralize this charge?
You should probably start over and check carefully for any warnings or error
messages. Which force field are you using? A charge of 0.08 sounds like a
missing hydrogen, but that may or may not be true.
-Justin
Thank you in advance.
--
Tehran University of Medical Sciences
www.tums.ac.ir
--
========================================
Justin A. Lemkul
Graduate Research Assistant
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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