[gmx-users] Fwd: Matching atom name and types in OPLS-aa FF
tree.csc at gmail.com
Sat Mar 14 01:53:15 CET 2009
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>
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
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
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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