Dear all, i'm making a .rtp for a sugar for the OPLS-AA force-field. To start i made a topology with the PRODRG server, so i have a list with all bonds, angles and dihedrals, but the problem is, that i'm missing the unpolar hydrogens. How to set up the bonds and angles entrys is no problem, but with the dihedrals i have problems.
If i have for example the the following molecule (should look like a double Y): L1\ /R1 L-R L2/ \R2 (L1 and L2 bounded to L, then L to R, and R is bounded to R1 and R2) In this case i have the dihedral between L and R, but i have 4 possibilities to set it up: L1-L-R-R1 L1-L-R-R2 L2-L-R-R1 L2-L-R-R2 So my problem is how to choose which possibility should i use. If L1, L2 and R1, R2 are equal there is no problem, because then the 4 possibilities are all equal. Hope somebody can help me. Greetings Thomas _______________________________________________ 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 gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
