<font color="#000099"><font face="verdana,sans-serif">This is a "reasonable" answer :)</font></font><div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">Thanks for that, and I just tried Gromacs for minimization, and looks the final structure does not have clashes anymore, and also are very close to the initial structure.</font></font></div>
<div><font color="#000099"><font face="verdana,sans-serif"><br></font></font></div><div><font color="#000099"><font face="verdana,sans-serif">Another question is if there is a way to add ions automatically, meaning no need to check the "NOTE" of "System has non-zero total charge" in the output of grompp command? And also update the topology file automatically too?<br>
</font></font><br><div class="gmail_quote">On Mon, Nov 14, 2011 at 3:49 PM, Justin A. Lemkul <span dir="ltr"><<a href="mailto:jalemkul@vt.edu">jalemkul@vt.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div class="HOEnZb"><div class="h5"><br>
<br>
Liu, Liang wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi, all,<br>
I am wondering if Gromacs can do the following work?<br>
<br>
Assuming I have a pdb file of an RNA molecule. Some atoms may be too close or even overlap, I am wondering if Gromacs can move the atoms to reasonable positions and remove the bad contacts? The final structure is supposed to be the "most" stable structure with minimal energy. I know AMBER minimization can do this work, and I am wondering if Gromacs can do the same?<br>
<br>
</blockquote>
<br></div></div>
Gromacs is perfectly capable of energy minimization. Whether or not minimization succeeds and gives a reasonable output is mostly dependent upon the feasibility of the starting structure. If the minimization crashes, it's not Gromacs' fault ;)<br>
<br>
-Justin<br>
<br>
-- <br>
==============================<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>
<br>
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</font></span></blockquote></div><br><br clear="all"><div><br></div>-- <br>Best,<br>Liang Liu<br>
</div>