Dear justin<br>after using grompp without -maxwarn I faced these:<br><br>NOTE 2 [file g-dist.mdp, line unknown]:<br> You are using a plain Coulomb cut-off, which might produce artifacts.<br> You might want to consider using PME electrostatics.<br>
<br><br>This run will generate roughly 2 Mb of data<br>writing run input file...<br><br>There were 2 notes<br><br>There were 3 warnings<br><br>-------------------------------------------------------<br>Program grompp, VERSION 4.0.7<br>
Source code file: ../../../../src/gmxlib/gmx_fatal.c, line: 481<br><br>Fatal error:<br>Too many warnings (3), grompp terminated.<br>If you are sure all warnings are harmless, use the -maxwarn option.<br><br>besides it is in 6454 line of complex.gro<br>
<br><br><br><br><br><br><div class="gmail_quote">On Tue, Dec 21, 2010 at 4:32 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="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
<div class="im"><br>
<br>
mohsen ramezanpour wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
Dear All<br>
I did the Enzyme/drug tutorial and generated complex.gro and complex.top files as was said.<br>
Now I want to measure the distance between center of mass of protein and drug<br>
I used g_dist but I could not.<br>
I entered these commands(of course I made an index.ndx and g-dist.tpr):<br>
<br>
I used from an typical .mdp file to generate .tpr file by below command:<br>
<br>
grompp -c complex.gro -p complex.top -o g-dist.tpr -f g-dist.mdp -maxwarn 3<br>
</blockquote>
<br></div>
What warnings are you ignoring? This is, in general, a very bad idea.<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
then,<br>
g_dist -f complex.gro -s g-dist.tpr -o g-dist.xvg<br>
<br>
but the result was an empty g-dist.xvg and:<br>
<br>
Fatal error:<br>
Unexpected end of file in file 631LIG C12 45 -0.475 -0.514 -0.434 at line 2<br>
(Source file ../../../../src/gmxlib/confio.<br>
c, line 725)<br>
<br>
</blockquote>
<br></div>
How many atoms are in complex.gro? To what line number does this atom entry correspond? It seems g_dist thinks the file should end here, prematurely.<br>
<br>
-Justin<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
besides,I want to measure this distance befor erunning and as a vector.<br>
below is a part of my complex.gro:<br>
631LIG F1 42 -0.701 -0.571 -0.151<br>
631LIG C16 43 -0.534 -0.501 -0.306<br>
631LIG H16 44 -0.491 -0.434 -0.232<br>
631LIG C12 45 -0.475 -0.514 -0.434<br>
631LIG H12 46 -0.394 -0.446 -0.459<br>
<br>
<br>
thanks in advances<br>
<br>
</blockquote>
<br></div>
-- <br>
========================================<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> | (540) 231-9080<br>
<a href="http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin" target="_blank">http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin</a><br>
<br>
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