[gmx-users] OPLSAA parameters
Justin A. Lemkul
jalemkul at vt.edu
Mon Aug 1 02:03:51 CEST 2011
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 <jalemkul at vt.edu
> <mailto:jalemkul at 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>
>
> ==============================__==========
> --
> gmx-users mailing list gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>
> http://lists.gromacs.org/__mailman/listinfo/gmx-users
> <http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at
> http://www.gromacs.org/__Support/Mailing_Lists/Search
> <http://www.gromacs.org/Support/Mailing_Lists/Search> before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org
> <mailto:gmx-users-request at gromacs.org>.
> Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
> <http://www.gromacs.org/Support/Mailing_Lists>
>
>
--
========================================
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
========================================
More information about the gromacs.org_gmx-users
mailing list