[gmx-users] mdsimulation of drug enzyme complex

abhijit kayal kayalabhijitiitd at gmail.com
Fri Apr 9 14:08:16 CEST 2010

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.

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