""" This depends entirely upon what your goal is. Your original question implied you wished to build a system of multiple, identical peptides, pertaining to:
http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Identical_chains Now you want a multimeric protein for which there are multiple, potentially different peptide, i.e.: http://www.gromacs.org/Documentation/How-tos/Multiple_Chains#Non-identical_chains The approaches are completely different, as the documentation should make quite clear. Simply "having multiple chains" is a very vague statement. Perhaps if you clearly stated your goal for the simulation I (or someone else) could help you better. As for the PDB site, there are probably thousands of proteins in line with what you want. Any heteromultimeric protein would do (assuming, of course, the latter case of non-identical chains). -Justin """ Sorry I wasn't clear. Basically I want to have a simulation box with as many of the same polypeptide as I can cram in, essentially a simulation of the polypeptide melted. I would like to see how the polypeptides interact with each other with the ultimate goal of simulating block copolymers. Since I'm new with Gromacs, I'm just trying to figure out how to run simulations with multiple chains where all chains are the same type. Justin, you've been very helpful so far and I appreciate it.
-- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
