dear all, till now i simulated with the gromos87 forcefield, but now i want to change it. i have two small molecules which consist of a short alkane chain and then an urea-group.
i built my molecules with spartan and saved them as .pdb then i tried pdb2gmx, but this failed: Fatal error: Residue 'UNK' not found in residue topology database but i have no idea how i should name the residues so that they are found in the database. then i tried pdb2gmx with my .gro file (which i get from prodrg with the .pdb file), but here the same problem occured. the other thing that i tried was to make the files with the beta version of prodrg. i get the .gro/.g96 and .itp files but they look the same like the files for the gromos87 forcefield (different values but the same format). i used editconf on the .g96 file but it doesn't really work, the new .g96 file looks like: TITLE END POSITION END BOX 10.000000000 10.000000000 10.000000000 END from that and the gromacs-user manual i get the idea that .gro and .96 files use different formats, but i don't really know how the format for .g96 looks like (i looked for a user manual for gromos96, but didn't found one for free). so the question is: 1) is there a way to translate the gromos87 files to gromos96? or 2) what should i do with the files form prodrg beta that they work? thanks for an answer thomas _______________________________________________ gmx-users mailing list [email protected] http://www.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
