Talk of each chain you have there as a molecule, which is what they are. So what you want is multiple molecules within the box, correct?
Once you start referring to them at molecules, then it should become far more obvious what you need to do. To do that, you take a single molecule in a coordinate file, then tell a script to put many copies of that molecule within a given box size. The GROMACS scripts to date have not really been the best for doing that, but genconf and genbox are the ones that you can use. Catch ya, Dr. Dallas Warren Medicinal Chemistry and Drug Action Monash Institute of Pharmaceutical Sciences, Monash University 381 Royal Parade, Parkville VIC 3010 [email protected] +61 3 9909 9304 --------------------------------- When the only tool you own is a hammer, every problem begins to resemble a nail. From: [email protected] [mailto:[email protected]] On Behalf Of C Johnson Sent: Thursday, 16 September 2010 8:32 AM To: [email protected] Subject: [gmx-users] Re Multiple Chains """ 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_c hains 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-identic al_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.
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