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

[tree]

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.

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
>> 
>>
>> 
>> ------------------------------------------------------------------------
>> 
>> _______________________________________________
>> gmx-users mailing list    gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before 
>> posting!
>> Please don't post (un)subscribe requests to the list. Use the www 
>> interface or send it to gmx-users-request at gromacs.org.
>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>
> -- 
> ========================================
>
> 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
> Please search the archive at http://www.gromacs.org/search before 
> posting!
> Please don't post (un)subscribe requests to the list. Use the www 
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>