Hi Stephan, <snip>
> I did this from the biggening, it's strait forward as you said. The problems > with the tutorials is they already work, and are missing a shlew of problems > one may incounter when doing more complicated things, etc... It must have been a disappointment while going for your drivers license, that the lessons didn't involve off road racing. But it's true: tutorials are meant for you to learn to walk. The running you'll have to get to yourself. Are you already up to that point? But what is actually so different about your system that makes it difficult to deal with using a standard (tutorial-like) protocol? Okay, the system is big, but that shouldn't be an issue. The sequence is the same (http://www.nmr.chem.uu.nl/~tsjerk/course/molmod/01-Preparation-Workflow.jpg), starting with generating topologies for your chains. In some cases, especially if building a topology for a chain requires some special attention, like setting protonation states or termini, it may be convenient to first split the structure into separate files, processing each separately to construct a topology. Going the opposite way, adding all pieces together, including solvent and ions and such, and then trying to get a complete topology for the whole lot in one go with pdb2gmx may easily get you in trouble. > I have a smart question though, why do computer folks have an insssesant need > to be correct, or smart, or image based things? Correct and smart is not by need, but just the way it is :p But an incessant need to be image based things? Hope it helps, Tsjerk -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group Groningen Institute for Biomolecular Research and Biotechnology University of Groningen The Netherlands -- gmx-users mailing list [email protected] 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 [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
