Mark Abraham ha scritto: > ms wrote: >> Mark Abraham ha scritto: >>> 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? > > make_ndx is the tool for generating such groups. If you read make_ndx -h > you'll see it does indeed let you create groups based around chain IDs, > but that'd (at least) require supplying it with a coordinate file that > has chain IDs. You could do that, but doing the house-keeping to assign > those IDs is tricky, and with PDB you're probably limited by 26 letters. > make_ndx will also let you create a group according to a range of atomic > numbers "a 1-10" or residue numbers "r 1-10". This avoids needing to > preserve/create chain IDs. Since you only need to create index groups > once for a given coordinate file, that's not too onerous. If you will > have lots of simulations with different numbers of such groups then you > might write a script to automate that... see > http://www.gromacs.org/Documentation/How-tos/Making_Commands_Non-Interactive >
Wonderful advice! (and also Justin Lemkul one). Thanks for your help. Do you mind if I later I try to update the "multiple chains" wiki page based on your advices? >>> 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 :) > > Sure. Doing some "irrelevant" tutorial material can be useful > introductions to the workflows. Regard;ess, the learning curve can be > steep for all computational chemistry software. Unfortunately no > beginner these days seems to want to come in and just do > protein-in-water :-) That makes their life hard. Yep, unfortunately that's kinda not simply "protein-in-water". I am trying to understand all pieces I need very slowly, step-by-step. And I guess you will hear my cries often in this ML :) Thanks again, 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
