Hi Justin,<div> No my ligand is different. And my topolgy look like this</div><div> #include "ffG43a1.itp"<div> #include "rrg.itp"</div>
<div> #include "drg.itp"</div><div> and at the end it is like this</div><div> </div> Protein 1<div>
RRG 1</div><div> DRG 1</div><div> SOL 17662</div><div> But I cannot understand where my topology is wrong.</div>
<div> What I did is that I docked a ligand at active site then another ligand at the active site. Then I separate the ligands coordinate and generate .gro,.itp file using PRODRG server.</div><div> Please reply </div>
<div> Abhijit</div><div> </div>
<div> </div><br><div class="gmail_quote">On Fri, Apr 9, 2010 at 6:33 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="im"><br>
<br>
abhijit kayal wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Hi<br>
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 <br>
</blockquote>
<br></div>
Be prepared to justify that the topology is "fine" to a reviewer. Every time I have generated a PRODRG topology, some aspect of its atom types, charges, or charge groups has been wrong. You always need to prove your parameters are valid (hence the link I posted) or else you are wasting a lot of time doing meaningless MD with a flawed physical model.<div class="im">
<br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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>
</blockquote>
<br></div>
I have no idea. Are your ligands different? The same? If they're the same, then there is absolutely no reason why you can't simply:<br>
<br>
#include "ligand.itp"<br>
<br>
[ molecules ]<br>
LIG 2<br>
<br>
Without seeing your topology or getting a better sense of what it is you did, there's not much more to offer. GROMACS isn't magically converting one molecule into two; somehow the instructions you're providing grompp and/or mdrun are causing the problem.<br>
<br>
-Justin<br>
<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">
On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul <<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a> <mailto:<a href="mailto:jalemkul@vt.edu" target="_blank">jalemkul@vt.edu</a>>> wrote:<br>
<br>
<br>
<br>
abhijit kayal wrote:<br>
<br>
Hello everybody,<br>
I am going to simulate an enzyme complex<br>
taking a ligand at active site and another ligand at allosteric<br>
site. When I ran md simulation taking ligand at active site only<br>
then it was ok. But when I am running the simulation taking both<br>
the ligand it is showing error "1-4 interaction between 3481 and<br>
3485 at distance 4.979 which is larger than the 1-4 table size<br>
2.000 nmThese are ignored for the rest of the simulation.This<br>
usually means your system is exploding,if not, you should<br>
increase table-extension in your mdp file or with user tables<br>
increase the table size". When I look the particular atoms they<br>
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<br>
not understand why GROMACS takes into account bcause they are<br>
far apart or is there any wrong to my pdb file. I am genereting<br>
the coordinate and topology using PRODRG server. I am also<br>
attached my input pdb file.<br>
Please help me to find out the problem.<br>
<br>
<br>
Have you looked into the list archive? This "blowing up" error has<br>
been reported, diagnosed, and solved hundreds (if not thousands) of<br>
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<br>
incorrectly, since your two separate ligands are being considered<br>
one molecule and thus experiencing intramolecular 1-4 interactions.<br>
Also note (as I've said dozens of times), face-value PRODRG<br>
topologies are often unsatisfactory (and thus unreliable) without<br>
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>
Abhijit<br>
<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></div></div>
jalemkul[at]<a href="http://vt.edu" target="_blank">vt.edu</a> <<a href="http://vt.edu" target="_blank">http://vt.edu</a>> | (540) 231-9080<div class="im"><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>
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<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>
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