Hi<div> Thank you for your quick reply. As you mentioned I went through the mailing list search. And I am thinking my error occured at the system preparation with taking the two ligands. Earlier I ran md simulation taking the ligand individually and it was showing no error. So the topolgy I got from the PRODRG server is fine. So input file may be error because GROMACS took both drug as a single one. So please help me how to take the input pdb file that it does not take a single ligand.<br>
<br><div class="gmail_quote">On Fri, Apr 9, 2010 at 5:46 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><div></div><div class="h5"><br>
<br>
abhijit kayal wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hello everybody,<br>
I am going to simulate an enzyme complex taking a ligand at active site and another ligand at allosteric site. When I ran md simulation taking ligand at active site only then it was ok. But when I am running the simulation taking both the ligand it is showing error "1-4 interaction between 3481 and 3485 at distance 4.979 which is larger than the 1-4 table size 2.000 nmThese are ignored for the rest of the simulation.This usually means your system is exploding,if not, you should increase table-extension in your mdp file or with user tables increase the table size". When I look the particular atoms they corrospond to the last atom of the ligand at the active site<br>
and the fourth atom the ligand at the allosteric site. So I can not understand why GROMACS takes into account bcause they are far apart or is there any wrong to my pdb file. I am genereting the coordinate and topology using PRODRG server. I am also attached my input pdb file.<br>
Please help me to find out the problem.<br>
<br>
</blockquote>
<br></div></div>
Have you looked into the list archive? This "blowing up" error has been reported, diagnosed, and solved hundreds (if not thousands) of times, and there are only a few reasons why it's happening. Also:<br>
<br>
<a href="http://www.gromacs.org/Documentation/Terminology/Blowing_Up" target="_blank">http://www.gromacs.org/Documentation/Terminology/Blowing_Up</a><br>
<br>
>From your description, it sounds as if the topology is constructed incorrectly, since your two separate ligands are being considered one molecule and thus experiencing intramolecular 1-4 interactions. Also note (as I've said dozens of times), face-value PRODRG topologies are often unsatisfactory (and thus unreliable) without modification of charges and charge groups. See here:<br>
<br>
<a href="http://www.gromacs.org/Documentation/How-tos/Parameterization" target="_blank">http://www.gromacs.org/Documentation/How-tos/Parameterization</a><br>
<br>
-Justin<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Abhijit<br>
<br>
</blockquote>
<br>
-- <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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