[gmx-users] where is water?

[Justin A. Lemkul]

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

-- 
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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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