[gmx-users] Matching atom name and types in OPLS-aa FF
Justin A. Lemkul
jalemkul at vt.edu
Sat Mar 14 02:06:04 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 opls_xxx.
It does, but only indirectly. Example, from ffoplsaa.rtp:
[ ACE ]
[ atoms ]
CH3 opls_135 -0.180 1
HH31 opls_140 0.060 1
opls_135 CT 6 12.01100 -0.180 A 3.50000e-01 2.76144e-01
opls_140 HC 1 1.00800 0.060 A 2.50000e-01 1.25520e-01
So the more literal interpretation of opls_135 is atom type CT, and opls_140 is
HC. I assume this is done for convenience.
Therefore, in ffoplsaabon.itp:
CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file
> 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.)
Nothing is typically done based on atom names; atom types are much more
important when considering bonded and non-bonded potentials.
> 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-?
Translate the opls_XXX atom types to a more "literal" type given in ffoplsaanb.itp.
> I hope my question and Englsh are clear enough...
> Thank you again!
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Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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