[gmx-users] mdsimulation of drug enzyme complex

Justin A. Lemkul jalemkul at vt.edu
Fri Apr 9 14:16:17 CEST 2010

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:


 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:



>   Abhijit


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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