[gmx-users] OPLS and RB parameters in GROMACS

[Rainer Boeckmann]

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 <apaluch at 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 <mssulatha at 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
> 
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__________________________________________________________
Prof. Dr. Rainer Böckmann
Computational Biology
Universität Erlangen-Nürnberg
Staudtstr. 5
91058 Erlangen
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E-Mail: rainer.boeckmann at biologie.uni-erlangen.de
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___________________________________________________________