[gmx-users] Structure Changed

[Sana Saeed]

hi gmx usersi am running MD of 1hsg (HIV II protease +MK1) A COMPLEX of chain A chain B and a ligand. i first separate the ligand and protein and docked then in Autodock Vina. and then made topology file of ligand by using Acpype.py, and protein's topology through pdb2gmx. i made complex of both coordinate files and included ligand.itp in Topol.top. after that i did generated box (-c -bt cubic -d 2.0) and solvated the system, i added ions , did Energy minimization, generated index file for protein and ligand complex and (used tc_groups as Protein_Ligand water_and_ions), position retrained my ligand and #define it in topol.top. did NVT , NPT and then MD. but when i visualize the result from trajectory file and gro file, the ligand structure is changed, also the atoms of some of the water molecules are moved away from each other. please help me what to do. these are my mdp filesSana Saeed