[gmx-users] Structure Changed

[Smith, Micholas D.]

The force-field you generated for the ligand may not be perfect, and as a result the ligand structure may alter during the energy minimization. Another thing to check is did you remember to make your molecules whole again before visualizing in vmd? 

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Micholas Dean Smith, PhD.
Post-doctoral Research Associate
University of Tennessee/Oak Ridge National Laboratory
Center for Molecular Biophysics

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From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sana Saeed <bioinformatic.lady at yahoo.com>
Sent: Wednesday, December 09, 2015 10:32 PM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Structure Changed

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