[gmx-users] RE: Position restraints

Thank you for responce and explanation! So is it a good alghorithm to use gromacs genrestr command and then include this posre.itp file into topology (without any changes) after insertion of a ligand.itp? Thank you in advance On 4/2/13 6:07 AM, alex rayevsky wrote: Dear All! I have a doubt

[gmx-users] Position restraints

Dear All! I have a doubt about the rightness of ligand/molecule integration in the topology file. I'm using an amber (tleap) or swissparam.ch to build a topology of the residue (modified trna). Is it neccessary to generate a position restrain file (genrestr program) for this residue or not? I've

[gmx-users] correct usage of freezing group

Hi dear All! Good day dear forum! I have a question abour freezing of atoms during MD. The idea is that - I have a protein and one domain contains a site. Also I have two ligands, one of them is better inhibitor in comparison with another one. To prepare the topology of the inhibitor I need to use