[gmx-users] Matching atom name and types in OPLS-aa FF
tree
tree.csc at gmail.com
Tue Mar 17 08:45:01 CET 2009
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?]
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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