Hi, I am inexperienced with gromacs and I would like to figure out the format of all parts of a .top file, needed for Gromacs. I am trying to understand the input format so I can write a program for automatic setup for small molecule ligands with Gromacs, using the oplsaa force field. I have recently written a C++ program that converts BOSS autoput and creates NAMD input. Now I would like to do a similar program for Gromacs.
I would like to write as few files as possible. I have some problems understanding the format of the dihedrals in the .top file. I have pasted the top file for methanol I have been preparing manually below. Please point out any errors. Any pointers would be greatly appreciated. Methanol 4 [atoms] 1 opls_157 1 UNK C00 1 -0.043617 2 opls_154 1 UNK O01 1 -0.586987 3 opls_156 1 UNK H02 1 0.074589 4 opls_156 1 UNK H03 1 0.074589 5 opls_156 1 UNK H04 1 0.074589 6 opls_155 1 UNK H05 1 0.406836 [bonds] 1 2 1 0.14100 267776.00 2 6 1 0.09450 462750.40 1 2 1 0.14100 284512.00 1 2 1 0.14100 284512.00 1 2 1 0.14100 284512.00 [angles] 4 1 2 1 109.50 292.880 5 1 2 1 109.50 292.880 6 2 1 1 108.50 460.240 3 1 2 1 109.50 292.880 4 1 5 1 107.80 276.144 5 1 3 1 107.80 276.144 5 1 4 1 107.80 276.144 [dihedrals] 6 2 1 3 3 ?? ... ?? If I want to add the 6-2-1-3 parameter in Ryckaert Bellman format, how do I enter the information in the dihedral part of the .top file? The RB parameters for 6-2-1-3 is given below: C0 = 0.94140 C1 = 2.82420 C2 = 0.00000 C3 = -3.76560 C4 = 0.00000 C5 = 0.00000 How do I enter this information into the .top file? Any help would be greatly appreciated! Thanks! Best, Markus -- 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