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

[XAvier Periole]

On Mar 16, 2009, at 9:34 AM, tree wrote:

> Dear Justin and All:
>
>
> I truly appreciate your clear answer.
> Since my questions are solved by your explanations, I do not know  
> how I can express my grateful heart.
>
> Now I have to ask second step questions. :)
> It is related to the OPLS-aa "bon.itp" file.
> Each section (bonds, angle, diherdal, and etc.) has its "type".
> I am wondering if this "type" (of course, in OPLS-aa case) has the  
> same meaning in the Gromos potentials.
> As we know, those types for each kind of bonded interactions are  
> well described in the Gromacs manual with clear equations.
> So, my question is (as I mentioned just above) if this is the same  
> as the OPLS-aa case.
Yes, the bond, angle, dihedral types are independent to the underlying  
force field
and correspond to the description in the manual.
>
> To make my question clear, I want to give an example.
>
> [ bonds ]
> ...
> CT	HC	1	0.10900	284512.0	; CHARMM 22 paramter
> ...
>
> I know the number "1" here means type, which describes what kind of  
> the bonds (strech) between two bonds is used.
> If this is Gromos potential, I am sure this "1" means "harmonic"  
> potential according to the Chap. 4 of the Gromacs manual.
> Is this also applied to OPLS-aa FF?
>
> Thank you for your care, again.
>
>
> Sincerely yours,
>
> Kim
>
> On Fri, 13 Mar 2009, Justin A. Lemkul wrote:
>
>>
>>
>> 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
>>
>> ========================================
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