Dear gmx users,
I am trying to manually make a topology file for a peptide with few substitutions. I had trouble in understanding regarding assignment of dihedral paramaters in opls by grompp. As far as I understood, ffoplsaabond.itp contains all the dihedral parameters where the bond_type from ffoplsaanb.itp are used to define the dihedral angles. If I take an entry from ffoplsaa.rtb for example glycine, [ GLY ] [ atoms ] N opls_238 -0.500 1 H opls_241 0.300 1 CA opls_223B 0.080 1 HA1 opls_140 0.060 1 HA2 opls_140 0.060 1 C opls_235 0.500 2 O opls_236 -0.500 2 And search for a dihedral H-CA-C-O in ffoplsbon.itp, I don't find any entries. Probably, I have to look for the bond_type corresponding to opls_??? entries and then search in ffoplsaabond.itp. It means that the first column entries in rtb file is only used to map PDB atom types to opls atom types and is of no further use. Please let me know if I am wrong. With Regards, Gurpreet Singh ------------------------------------------------- University of Dortmund Department of Chemistry Physical Chemistry I - Biophysical Chemistry Otto-Hahn Str. 6 D-44227 Dortmund Germany Office: C1-06 room 176 Phone: +49 231 755 3916 Fax: +49 231 755 3901 -------------------------------------------------
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