[gmx-users] coenzyme-protein complex

Mostafa Javaheri 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?
M. Javaheri

More information about the gromacs.org_gmx-users mailing list