[gmx-users] coenzyme-protein complex
m.javaheri at gu.ac.ir
Mon Jan 6 11:40:40 CET 2014
Dear Gromacs users
I would be grateful if any one answers my questions
I have two coenzyme (GTP & GDP) and two Ion (Mg) attached to the
hetrodimer protein, I am going to use charmm27 force field for Gromacs simulation and swissparam for achieving the ligands topologies; Could I trust at these topology (.itp) or they need
some charge correction like PRODRG outputs?
2. Does anyone have ".mdp" fiels that consist with my system?
3. I merged these two ligands into one mol2 file and
sent it to the swissparam, then followed the rest of steps, is this OK or
should I send them separately?
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