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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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