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

[Tree]

Since I cannot see my message on the gmx-users mail list, I am forwarding
this again.I am sorry to bother your email box again...

Hope you would understand...

---------- Forwarded message ----------
From: Tree <tree.csc at gmail.com>
Date: Fri, Mar 13, 2009 at 8:51 PM
Subject: Matching atom name and types in OPLS-aa FF
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Cc: Chansoo Kim <tree.csc at gmail.com>


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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