Greetings all, I am trying to learn/use GROMACS for evaluating ligand dockings.
After some effort I managed to get a run through EM, equilibration and production with protein and water. I am now having some difficulty getting a similar run going with a ligand. I am not ready to talk about the specific problems I am having but I was wondering if someone could check my approach/methodology is correct and if I am doing something GROMACS doesn't like/fundamentally wrong. I have an .itp from the ATB. I take my .pdb and remove the ligand. I run PDB2GMX on the no_lig.pdb and get a .top and a new no_lig2.pdb I edit the .top and add #include "lig.itp" I use editconf on the no_lig2.pdb -bt cubic -d 0.5 I use genbox to insert the lig.pdb into the no_lig2.pdb and get complex.pdb I use genbox to solvate complex.pdb and return complex.gro as well as an updated .top I use grompp to process my em.mdp .top and complex.gro and get complex.tpr <- (my current problem step) I use mdrun complex.tpr and get my trajectory repeat last two steps for equilibration and production. I have not used genion yet, I assumed that it would affect the simulation accuracy but not its ability to run, I am currently +13. I also realise that I do not have position restraint files for the ligand at the moment so equilibration wont be correct. all the best, Tom-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
