[gmx-users] Matching atom name and types in OPLS-aa FF

Tree tree.csc at gmail.com
Sat Mar 14 01:51:44 CET 2009

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
"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
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!


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