[gmx-users] mdsimulation of drug enzyme complex

abhijit kayal kayalabhijitiitd at gmail.com
Fri Apr 9 14:32:57 CEST 2010

      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.

On Fri, Apr 9, 2010 at 5:46 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

> abhijit kayal wrote:
>> Hello everybody,
>>                         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
>> 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.
>> Please help me to find out the problem.
> 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:
> http://www.gromacs.org/Documentation/Terminology/Blowing_Up
> 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:
> http://www.gromacs.org/Documentation/How-tos/Parameterization
> -Justin
>>  Abhijit
> --
> ========================================
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> ========================================
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