<http://gromacs.5086.n6.nabble.com/file/n5001418/Screenshot-2.png> This is the distance of one pair of atoms that i restraint. I apologize if i did't mention why i am using distance restraint, i am working with a protein obtained using homology modelling, the next step after i get the protein structure is doing molecular docking, the problem is that i need to refine the structure and i found in literature that the protein goes through a conformational change where it forms a bundle of 4 alfa helix (hydrofobic interactions) before it interacts with its ligand, so besides of making the refinment of the structure i need to obtain that bundle in order to do molecular docking. The reason for doing the refinement in vacuo is that when you minimize a struture to avoid steric clashes i always make them in vacuo with other software, the problem is that i need to form the bundle and the software i usually used doesn't handle position restraint. My intention never was to bother you, I am very thankful for your time to answer my questions. Sorry for all the inconvenience
Paula -- View this message in context: http://gromacs.5086.n6.nabble.com/distance-restraint-tp5001387p5001418.html Sent from the GROMACS Users Forum mailing list archive at Nabble.com. -- 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