Elisabeth wrote:
Thanks Justin for your guidance. By following your tips, I have now all
the parameters I need... Please let me know if I am missing any [
angletypes ] or [ dihedraltypes ] for a hydrocarbon molecule.
Seems fine to me; grompp will complain if something is missing. Is there a
reason that you're trying to parse out certain parameters? It'd be far easier
to just #include "oplsaa.ff/forcefield.itp" in your topology and have the entire
OPLS-AA force field available to you, rather than reinventing the wheel.
-Justin
Best,
[ bondtypes ]
; i j func b0 kb
CT CT 1 0.15290 224262.4 ; CHARMM 22 parameter file
CT HC 1 0.10900 284512.0 ; CHARMM 22 parameter file
[ angletypes ]
;i j k func th0 cth
CT CT CT 1 112.700 488.273 ; CHARMM 22 parameter file
CT CT HC 1 110.700 313.800 ; CHARMM 22 parameter file
HC CT HC 1 107.800 276.144 ; CHARMM 22 parameter file
[ dihedraltypes ]
CT CT CT CT 3 2.92880 -1.46440 0.20920
-1.67360 0.00000 0.00000 ; hydrocarbon all-atom
CT CT CT HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; hydrocarbon all-atom
HC CT CT HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; hydrocarbon *new* 11/99
On 30 July 2011 07:40, Justin A. Lemkul <jalem...@vt.edu
<mailto:jalem...@vt.edu>> wrote:
Elisabeth wrote:
Hello to all,
I am looking for bonded and nonbonded parameters for C H atoms
in saturated hydrocarbons.
atom types are:
Carbon atoms opls_135 opls_136 H opls_140
opls_135 12.01100 ; alkane CH3
opls_136 12.01100 ; alkane CH2
opls_140 1.00800 ; alkane H.
Please help me out with the following:
- I am wondering if I am selecting the correct values, for C-C
and C-H bonds from ffoplsaabon.itp.
The C-C bond is not correct for alkanes. It is for the C-C bond of
oxalic acid, as the comment indicates. In ffnonbonded.itp, you can
see how opls_* types are mapped to different bonded atom types (for
instance, opls_135/136 are CT). Note that in the topology, you do
not have to explicitly define values when using OPLS-AA; any bond
between two defined bonded atom types will be automatically detected
and used.
C C 1 0.15100 292880.0 ; wlj oxalic acid, etc.
HC C 1 0.10900 284512.0 ; wlj 7/96
- what does wlj mean?
Probably someone's initials, which occur frequently to indicate
either the source of the parameters or the individual that added
them. In this case, my guess would be Jorgensen is the referenced
individual here.
- what are the units?
This is in the manual.
Angle
CA CA CZ 1 120.000 585.760 ; wlj
CA CA CR 1 120.000 527.184 ;
CA CA CX 1 120.000 711.280 ;
C CT Cl 1 109.800 577.392 ; wlj
- I can not distinguish CA CZ .... What are they referring to?
See the above tip about converting atom types in ffnonbonded.itp.
[ dihedraltypes ]
C C CT HC 3 0.17782 0.53346 0.00000
-0.71128 0.00000 0.00000 ; dicarbonyls BMC 8,1881(2000)
- Is this what I need for oplsaa 135 136 140?
Probably not. The comment indicates the dihedral is for
dicarbonyls. The appropriate dihedral is:
CT CT CT HC 3 0.62760 1.88280 0.00000
-2.51040 0.00000 0.00000 ; hydrocarbon all-atom
Note how the comment indicates it is for use with hydrocarbons.
Again, like bonds as described above, you do not need to explicitly
list parameters in the topology. They will be inferred from the
atom types.
ffoplsaanb.itp.
opls_135 CT 6 12.01100 -0.180 A
3.50000e-01 2.76144e-01
opls_136 CT 6 12.01100 -0.120 A
3.50000e-01 2.76144e-01
opls_140 HC 1 1.00800 0.060 A
2.50000e-01 1.25520e-01
- are these parameters for
opls_135 12.01100 ; alkane CH3
opls_136 12.01100 ; alkane CH2
opls_140 1.00800 ; alkane H.
?
Yes.
Also in usr/local/gromacs/share/__gromacs/top/ directory I can
not find ffoplsaanb,itp and ffoplsaabon.itp for 4.5.4 whereas in
previous versions these files were accessible. I am using itp
files from version 4.0.7 and wanted to make sure the above
parameters for oplsa_135 oplsa_136 and oplsa_140 have been
remained unchanged in 4.5.4. Where can I find these files?
The force field organization has changed, but the content of the
force fields has not. This is described in the manual. All the
equivalent files are now in the oplsaa.ff subdirectory. For
backwards compatibility, the statement #include "ffoplsaa.itp" will
indeed call the force field, because you will note that ffoplsaa.itp
now simply calls the correct force field with #include
"oplsaa.ff/forcefield.itp."
-Justin
--
==============================__==========
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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
<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
==============================__==========
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========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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