Ragothaman Yennamalli wrote:
Hi Friends,
When I run pdb2gmx, it automatically asks which water topology should be
included. Also, in the .top file the lines included are:
; Include water topology
#include "gromos53a6.ff/spc.itp"
However, I do not see any water molecules in the .gro file. So, was
water included or not?
pdb2gmx does not add water. That's what genbox does. The water selection
utility in pdb2gmx is intended to make your life easier when it comes to
solvation - the water topology is already present (#included in the .top).
-Justin
--
========================================
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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