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. Abhijit
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