Dear Sulatha, these are probably the more recent parameters from
Price, M. L. P., D. Ostrovsky, and W. L. Jorgensen. 2001. Gas-phase and liquid-state properties of 8esters, nitriles, and nitro compounds with the opls-aa force field. J. Comput. Chem. 22:1340– 1352. Best Rainer On Feb 9, 2011, at 6:48 AM, sulatha M. S wrote: > I looked at the the paper published in 1999, ( Jorgensen et al JACS, 121, 20, > 4831, 1999), the aliphatic torsional parameters are the same as those from > 1996. here are the values, > > > V1 V2 > V3 (kcal/mol) > CT-CT-CT-CT 1.740 -0.157 0.279 > > HC-CT-CT-CT 0.000 0.000 0.366 > > HC-CT-CT-HC 0.000 0.000 0.318 > > > Values calculated from the equation given in p.62 of the manual in kJ/mol are > > c0 c1 > c2 c3 > CT-CT-CT-CT 3.56686 -1.88907 0.65688 > -2.33467 > > HC-CT-CT-CT 0.66526 1.99577 0.000 > -2.66102 > > HC-CT-CT-HC 0.76567 -2.29702 0.000 > -3.06269 > > and the values given in ffoplsaabon.itp are: > > CT-CT-CT-CT 2.9288 -1.4644 0.2092 > -1.6736 > > HC-CT-CT-CT 0.6276 1.88280 0.000 > -2.5104 > > HC-CT-CT-HC 0.6276 1.8828 0.000 > -2.5104 > > So there is a difference. Which of these is correct ? Any help is highly > appreciated. > > Sulatha > > > > On Tue, Feb 8, 2011 at 7:48 PM, Andrew Paluch <apal...@nd.edu> wrote: > There is no error. The alkane dihedral parameters were updated in 1999, and > differ from those originally published in 1996. > > Andrew > > On Tue, Feb 8, 2011 at 5:20 AM, sulatha M. S <mssula...@gmail.com> wrote: > Hi all, > Hi > > I've converted the OPLS-AA torsional potential parameters for the > alkane C-C-C-C (CT-CT-CT-CT in the gromacs parameter file notation), > C-C-C-H (CT-CT-CT-HC), and H-C-C-H (HC-CT-CT-HC) torsions from the > OPLS format given in Jorgensen et al, JACS 118, 11225 (1996) > to the Ryckaert-Bellemans format given in ffoplsaabon.itp and found > that the calculated values are different. > > A previous post to the gmx-users mailing list on March 27, 2008, > pointed out this issue for the H-C-C-H torsional potential but there was no > response to that. > > Does anyone know if there is an error in the ffoplsaabon.itp file? Or > is there a newer set of OPLS-AA parameters? > > For the OPLS-AA parameters (in kcal/mol), I used: > > dihedral V1 V2 V3 > C-C-C-C 1.740 -0.157 0.279 > C-C-C-H 0.0 0.0 0.366 > H-C-C-H 0.0 0.0 0.318 > > from which I calculated the Ryckaert-Bellemans parameters (in kJ/mol) as: > > dihedral C0 C1 C2 C3 > C-C-C-C 3.56686 -1.889076 0.65688 -2.33467 > C-C-C-H 0.66526 1.99577 0.0 -2.661024 > H-C-C-H 0.76567 -2.29702 0.0 -3.06269 > > the parameters in the ffoplsaabon.itp file are: > > dihedral C0 C1 C2 C3 > C-C-C-C 2.9288 -1.4644 0.2092 -1.6736 > C-C-C-H 0.6276 1.88280 0.0 -2.5104 > H-C-C-H 0.6276 1.8828 0.0 -2.5104 > > > Thankyou for any clarification. > > Sulatha > > -- > 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 > > > -- > 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 > > -- > 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 __________________________________________________________ Prof. Dr. Rainer Böckmann Computational Biology Universität Erlangen-Nürnberg Staudtstr. 5 91058 Erlangen Phone: ++49 +9131 85-25409 FAX: ++49 +9131 85-25410 E-Mail: rainer.boeckm...@biologie.uni-erlangen.de http://www.biotechnik.nat.uni-erlangen.de/research/boeckmann/ ___________________________________________________________ -- 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
