> Justin A. Lemkul wrote: >> >> I have also added a Perl script to the GROMACS site (the VMD page): >> >> http://www.gromacs.org/Developer_Zone/Programming_Guide/VMD >> >> The user provides an input topology file, and a .psf file is written, >> which can be loaded as data for the structure in VMD. The !NBOND >> section seems to be the most important in this regard, so the other >> sections are a bit rough, but it seems to work alright. >> >> The caveat is the topology must be one generated by MARTINI, in order to >> satisfy all the pattern matching and the order of the topology. It >> should be fairly easy to modify the program further to accommodate other >> layouts, but I haven't had the need to do so. > > I added text to the above page describing both scripts, which are > attached. I'd have done that yesterday but the website was > intermittently down.
Thanks for posting the tcl script on the website, although this script has been mainly coded by someone else. I have simply modified it for my own purpose. I also want to mention it is a good think to create a psf file if one work with VMD. You store at once, bonds, atom types and charges. Actually, I should have somewhere a .rtf file for the Martini amino acids and lipids (the equivalent of the Gromacs rtp file for CHARMM). It can be used by psfgen to generate a psf file with Martini bonds, charges and atom types. If I can retrieve it in my archives, I will post it on the website. Nicolas > > Mark > >> Nicolas Sapay wrote: >>> Hello Thomas, >>> >>> I have a tcl script in my personal script library that might do what >>> you want to do. I didn't use it for quite a while, but it was working >>> well as far as I remember. I think it has been adapted from a script >>> available on the VMD website, but I don't remember exactly its >>> history. It doesn't seem too difficult to understand. You should be >>> able to modify it for your own purpose, if needed. >>> >>> Cheers, >>> Nicolas >>> >>> >>> Thomas Schmidt a écrit : >>>> Dear Omer, >>>> >>>> many thanks for your answer, but your solution doesn't work for me. >>>> We have Protein-Lipid models in the CG scale. >>>> Only if I replace all atom names in the PDB file through "CA" I can >>>> use >>>> the "trace" drawing method, but get also wrong atoms connected to each >>>> other. For example CG Beads with low distances to each other, e.g. in >>>> coarse-grained benzene rings, were not connected. I guess that this >>>> method is distance dependent, too, but in another way. :-) >>>> >>>> Does anybody else have a solution (...to put GROMACS bond information >>>> into VMD)? >>>> >>>> Thomas >>>> >>>> >>> >>> _______________________________________________ >>> 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 >> > _______________________________________________ > 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 > > -- [ Nicolas Sapay - Post-Doctoral Fellow ] CERMAV - www.cermav.cnrs.fr BP53, 38041 Grenoble cedex 9, France Phone: +33 (0)4 76 03 76 44/53 _______________________________________________ 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
