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
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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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