Dear All:
I appreciate your answer always. Right now, I am trying to add/modify some values in OPLS-aa FF. I am confused atom type (opls_xxx) and atom name (e.g., C) in "atp", "bon.itp", and "nb.itp" files. Please let me try the situation by an example, first. In "atp" file, ... opls_058 12.01100 ; C in COOR ester JPC3315(91) opls_059 15.99940 ; O= in COOR ester ... In "bon.itp" file, ... C CA 1 0.14900 334720.0 ; wlj 8/97 C_2 CA 1 0.14900 334720.0 ; wlj 8/97 ... In "nb.itp" file, ... opls_009 C2 7 14.02700 0.000 A 3.90500e-01 4.93712e-01 ; SIG opls_010 C3 6 15.03500 0.000 A 3.90500e-01 7.32200e-01 ; SIG ... I hope you can sense what my question is here. When I define a residue in "rtp" file, I give some name for my atom in my system and assignment between that specific atom name and opls_xxx. Then, gromacs (pdb2gmx) is using "rtp" file to assign each atom to the opls_xxx. "nb.itp" also has opls_xxx information inside, so I can understand how those values are assigned. However, I am not clear how the procedue assign bonded potentials to the system, because "bon.itp" file does not have any information related to the opls_xxx. Also, my question related to the above sentece is whether the bonded potentials are assigned according to the name of atom, which I defined in my "pdb" file. (I doubt this... If this question is true, it can't be used for general cases.) This is subsequently how I can add new values in the "bon.itp" file by assigning the name in an appropriate way... I think I am relatively clear in assigning between opls_xxx and name in "nb.itp" file. To summarize my question, how the assignment between opls_xxx and name in the "bon.itp" can be defined-? I hope my question and Englsh are clear enough... Thank you again! Sincerely, Kim
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