Dear Rainer, Thankyou very much. I read the abstract of this paper and it says torsional parameters fro alkanes have been updated. I do not have access to full contents of this paper, so could not get it. Thanks again.
Sulatha On Wed, Feb 9, 2011 at 2:27 PM, Rainer Boeckmann < rainer.boeckm...@biologie.uni-erlangen.de> wrote: > 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<rai...@bioinformatik.uni-saarland.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 >
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