[gmx-users] Matching atom name and types in OPLS-aa FF
Tree
tree.csc at gmail.com
Tue Mar 17 01:47:20 CET 2009
Dear Dr. Periole:
Thank you for your answer.
You meant that the types of potential functions do not have any relations
with OPLS-aa (except first ("1") case).
Those (from "2"...) are defined as written the Gromacs manual.
Thank you again.
Sincerely,
Kim
On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> 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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