[gmx-users] opls bonded parameters

singh singh at biophysik.chemie.uni-dortmund.de
Wed Nov 28 17:31:23 CET 2007

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
Office:   C1-06 room 176
Phone:  +49 231 755 3916

Fax:     +49 231 755 3901



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