[gmx-users] Matching atom name and types in OPLS-aa FF
Tree
tree.csc at gmail.com
Wed Mar 18 01:48:28 CET 2009
Dear Dr. Periole:
Thank you for your answer.
That was the point which I wanted to double check (of course after reading
the manual...).
Thank you again!
Sincerely,
Kim
On Tue, Mar 17, 2009 at 6:09 PM, XAvier Periole <x.periole at rug.nl> wrote:
>
> On Mar 17, 2009, at 8:45 AM, tree wrote:
>
> Dear Justin:
>>
>>
>> Thank you for your email!
>>
>> Thanks to your help and explanation, I am feeling more comfortable with
>> OPLS topology modification.
>> Before this work, I have used Gromacs without modifying FF paramters for
>> simulating 'water' in general systems, which can easily obtained from PDB
>> sites.
>> So, it was not too easy to generate a sort of new topology even I've
>> learned MD.
>>
>> I understand what you meant here. :)
>> I did not mean the selection "1" (Harmonic potential function) is a sort
>> of OPLS-aa FF functions.
>> My question is actually if I can use the Forth power potential when I
>> choose "2" in bond streching section.
>> Since this funtion has different from from "1" (Harmonic potential
>> function), I thought that it may need other paramters that may (may not) be
>> different from the given parameters in OPLS-aa FF.
>> So, my question here is
>> [can I use the Forth power potential for bond strech using the given
>> OPLS-aa paramters?]
>>
> To that the answer is no! If you change the potential to describe a bond,
> angle ...
> the parameters will be different! Have a look a the manual chapter 4.
>
> I assume this would be same to others, angle, dihedral, and etc.
>>
>> Thank you again.
>>
>>
>> Sincerely,
>>
>> Kim
>>
>> On Mon, 16 Mar 2009, Justin A. Lemkul wrote:
>>
>>
>>>
>>> Tree wrote:
>>>
>>>> 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.
>>>>
>>>
>>> Table 5.4 defines the different types of intramolecular interactions.
>>> You should specify the proper terms based on what corresponds to the force
>>> field functional form. That is harmonic potential does not necessarily
>>> imply OPLS, but OPLS might imply that you have to use a harmonic potential
>>> (because, in fact, many force fields use a harmonic potential for bonds, not
>>> just OPLS!)
>>>
>>> You should refer to the primary literature for the force field, how it
>>> was derived, and any subsequent references regarding modifications to the
>>> force field.
>>>
>>> Another option (in addition to doing the background reading!) is to run
>>> through some tutorial material with a simple protein under OPLS to get a
>>> feel for how an OPLS topology is automatically created by pdb2gmx.
>>>
>>> -Justin
>>>
>>> Thank you again.
>>>> Sincerely,
>>>> Kim
>>>> On Mon, Mar 16, 2009 at 5:42 PM, XAvier Periole <x.periole at rug.nl<mailto:
>>>> 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 <http://vt.edu/> | (540) 231-9080
>>>> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>>>
>>>> ========================================
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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
>>>
>>> ========================================
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
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>
>
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