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.
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> 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 | (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@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-requ...@gromacs.org. > Can't post? Read > http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >
-- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at 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-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
