Thanks...Glad to realize the newer version of gromacs makes life easier.<br>Raghu<br><br><div class="gmail_quote">On Mon, Jul 11, 2011 at 11:38 AM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br>
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<br>
Ragothaman Yennamalli wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi Friends,<br>
<br>
When I run pdb2gmx, it automatically asks which water topology should be included. Also, in the .top file the lines included are:<br>
<br>
; Include water topology<br>
#include "gromos53a6.ff/spc.itp"<br>
<br>
However, I do not see any water molecules in the .gro file. So, was water included or not?<br>
<br>
</blockquote>
<br></div></div>
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).<br>
<br>
-Justin<br>
<br>
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==============================<u></u>==========<br>
<br>
Justin A. Lemkul<br>
Ph.D. Candidate<br>
ICTAS Doctoral Scholar<br>
MILES-IGERT Trainee<br>
Department of Biochemistry<br>
Virginia Tech<br>
Blacksburg, VA<br>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> | <a href="tel:%28540%29%20231-9080" value="+15402319080" target="_blank">(540) 231-9080</a><br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.<u></u>vt.edu/Pages/Personal/justin</a><br>
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