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

[XAvier Periole]

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.peri...@rug.nl <mailto:x.peri...@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

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