[gmx-users] Matching atom name and types in OPLS-aa FF
XAvier Periole
x.periole at rug.nl
Tue Mar 17 10:09:25 CET 2009
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
>> http://www.gromacs.org/mailman/listinfo/gmx-users
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>>
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