Mark Abraham ha scritto: > ms wrote: >> Hi, >> >> I am a gmx newbie, so please don't bite too much! :) >> >> Learning gmx, I am experimenting with simulations with multiple >> identical small chains. What I did was: >> >> - I generated the peptides with pymol >> - Generated a .gro with pdb2gmx > > This step is "generating a molecular topology". You don't need a .gro - > it's just a regularized coordinate file produced as a side-effect.
Very much right. Thanks. >> - Used editconf to create translated copies > > Try genconf to do the replication. That should remove much of the manual > labour. You would still probably need to edit in the chain IDs yourself, > but that's easy work with a script or good editor. Thanks! >> - Stitching them together and creating the complete file, adjusting >> numbers etc. manually >> >> It worked well, but the chains are not recognized as *different* chains >> -which could be useful. Documentation says I should use another format >> like the pdb, but it is a bit sparse on the subject. I think I can use >> pdb instead of gro if needed, but does this also work when creating >> boxes etc.? Isn't there a way to get chain identifiers in a gro file? >> What is best practice? > > What do you want the chain identifiers for? I'm not aware of a > post-pdb2gmx purpose that they might serve. This is where my naivety probably enters in: Analysis programs work on groups. If several chains are defined, can each of these count as a group? Indeed, chapter 8 doesn't explicitly say so, but... My intention is to get analysis for each chain in my system. What is best practice for that / where should I look in the docs? > If your system is N identical peptides in a solvent, then best practice > for generating a complete .top is to generate one for a single peptide > in solvent (e.g. pdb2gmx - editconf - genbox). Then generate a > coordinate file which contains the N peptides' coordinates followed by > all the solvent (e.g. genconf - genbox). Then edit the [ molecules ] > section of the original .top to match. Other solutions are possible, but > require more involved use of pdb2gmx, and might indeed want chain IDs. Uh, thanks. Not sure to have understood all of it, but I will do my homework before coming back :) m. _______________________________________________ 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/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/mailing_lists/users.php
