Dear GROMACS user: We downloaded the AMBER-03* potential parameters files (ffamber_v3.3.1-doc.tar.gz) linked with the page http://folding.stanford.edu/ffamber/index.html#validation. We tried to simulate the Dickerson dodecamer using the 3.3.1 gromacs version. Our simulation crash when we run the grompp program. A (nonexistent) error in the atom numeration of the topology is indicated by the program. Previously, we run the pdb2gmx and the genbox programs solving notation errors. Finally .top and coordinate files are generated without (apparently) errors. Analyzing the procedure, we observed that the format of the input files of the AMBER-03* potential (.rtp,.itp, etc.) frequently do not coincide with the input files included in the share/top folder of gromacs. For example the ffamber03.rtp file describe the bonds: .... [ bonds ] H5T O5' O5' C5' C5' H5'1 C5' H5'2 C5' C4' C4' H4' .... omitting the indication of the bond type, how for example occurs in ffG43a1.rtp ..... [ bonds ] N H gb_2 N CA gb_20 CA C gb_26 C O gb_4 ....... The list of differences is long, and this is only one example.
The questions are: a) There are any document indicating the format of the file inputs for the gromacs programs? The user manual 3.3 include little or not at all about this. b) Is the cause of the error these format differences? Thanks in advance Mario Campo and Griselda Corral Fac. de Cs. Exactas y Naturales UNLPam _______________________________________________ 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
