Dear Gromacs users I am currently preparing an RTP file to describe a polymer for use with MARTINI.
MARTINI does not include default bonded interactions, so all bonds, angles and dihedrals must be explicitly defined in the topology file or, in my case, in the RTP file. The problem is that pdb2gmx generates at least one dihedral for each bond and an angle for each pair of bonds sharing an atom, even it they are not explicitly defined in the RTP. In that case, pdb2gmx will include the triplet (or quadruplet) for the angle (or dihedral), but with empty parameters, so that grompp looks for general parameters in the forcefield ITP file. With coarse-graned forcefields, it does not necessarily make sense to have all angles and dihedrals, since, for example, rings are modelled as triangles of beads (so that the angles are redundant with the bond lengths) and trans alkyl chains are modelled as colinear beads (such that a dihedral is undefined). Is there a way to prevent pdb2gmx from creating these angles and dihedrals, unless explicity defined in the RTP? Also, the manual states the following regarding RTP files: "The first field in the file is the [ bondedtypes ] field, which is followed by four numbers, indicating the interaction type for bonds, angles, dihedrals, and improper dihedrals. " And includes this as an example: [ bondedtypes ] ; mandatory ; bonds angles dihedrals impropers 1 1 1 2 ; mandatory But the aminoacids.rtp file included in the opls-aa forcefield starts with: [ bondedtypes ] ; Col 1: Type of bond ; Col 2: Type of angles ; Col 3: Type of proper dihedrals ; Col 4: Type of improper dihedrals ; Col 5: Generate all dihedrals if 1, only heavy atoms of 0. ; Col 6: Number of excluded neighbors for nonbonded interactions ; Col 7: Generate 1,4 interactions between pairs of hydrogens if 1 ; Col 8: Remove propers over the same bond as an improper if it is 1 ; bonds angles dihedrals impropers all_dihedrals nrexcl HH14 RemoveDih 1 1 3 1 1 3 1 0 Which is inconsistent with the manual. In particular, Col8 set to 1 seems to remove dihedrals over bonds with any dihedral, not only those defined under the [ impropers ] directive. Could anyone clarify the role of these extra columns? I think this also hints for a review in this section of the manual. Thanks! -- Elton Carvalho Faculty of mathematics and natural sciences University of Groningen -- 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/Support/Mailing_Lists/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/Support/Mailing_Lists
