> Dear GROMACS users! > > Is it possible to model DNA with the help of GROMACS with AMBER ports? > I've checked mailing-list and found that the only GROMCAS force field > appropriate for modeling DNA is OPLS, but it does not provide good > enough results for long DNA MD runs. > The mailing-list suggested AMBER ports. I've managed to produce > topology and coordinates files, solvate the system. But when I came to > grompp step, I got the following error message: > > Program grompp, VERSION 3.3.1 > Source code file: grompp.c, line: 448 > > Fatal error: > number of coordinates in coordinate file (genbox.gro, 32804) > does not match topology (dick.top, 0) > --- > I've checked my dick.top file and it looks OK.
Unfortunately, it probably isn't... see http://wiki.gromacs.org/index.php/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology > I've also checked > ffamber99.rtp, ffamber99.atp, ffamber.hdb,ffamberbon.itp and several > other files. I am not a programmer myself, but I checked the same sort > of files for GROMOS force fields, they have different format Yeah, that's fine. > and I > suspect that this is the reason for the error message. The program > simply can't parse some files. > Has someone tried modelling DNA in GROMACS with AMBER ports? Was it > successful? Don't know. Mark _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
