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

[Justin A. Lemkul]

Tree wrote:
> 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.

It does, but only indirectly.  Example, from ffoplsaa.rtp:

[ ACE ]
  [ atoms ]
    CH3    opls_135   -0.180     1
   HH31    opls_140    0.060     1

 From ffoplsaanb.itp:

  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.

-Justin

> 
> I hope my question and Englsh are clear enough...
> 
> Thank you again!
> 
> 
> Sincerely,
> 
> Kim
> 
> 
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-- 
========================================

Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================