Hi All, I was trying *GROMACS Tutorial for Drug – Enzyme Complex* by *John E. Kerrigan* over one docked complex in following way. I generated topology and gromacs co-ordinates for ligand and cofactor successfully using PRODRG beta. Protein file is processed through "pdb2gmax_d" and resulted .gro and .top files are modified with PRODRG output (keeping *Chirality- yes, **Charges-full, EM-No*) as instructed in tutorial. Now when I am processing the modified .gro file to generate box, the ligand and cofactor are going away from the protein molecule and I am not able to analyze the complex. Can anybody help me to find the reason for this situation, Is it because of PRODRG options or something else?
If it i sbecause of modified co-ordinates from PRODRG, how can i keep the co-ordinates unchanged? I have done same exercise successfully with other molecules earlier. Any help or experience regarding this problem is highly appreciated. With tHanks, Vivek
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