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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