Thanks...Glad to realize the newer version of gromacs makes life easier. Raghu
On Mon, Jul 11, 2011 at 11:38 AM, Justin A. Lemkul <[email protected]> wrote: > > > 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<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin> > > ==============================**========== > -- > gmx-users mailing list [email protected] > http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> > Please search the archive at http://www.gromacs.org/** > Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before > posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to [email protected]. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
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