[gmx-users] mdsimulation of drug enzyme complex

[Justin A. Lemkul]

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
>                       
>        
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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