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 >
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