[gmx-users] OPLS and RB parameters in GROMACS
sulatha M. S
mssulatha at gmail.com
Wed Feb 9 07:33:25 CET 2011
Sorry for not giving the manual version earlier. P. 63 of manual 4.0 is what
I am referring to. The equations relate to converting the OPLS torsional
parameters to RB parameters in GROMACS with the OPLS ff.
The equations are
C0 = V0+V2+0.5(V1+V3)
C1= 0.5(3 * V3-V1)
C2= -V2 + 4 * V4
C3= -2 * V3
C4= -4 * V4
Thanks
Sulatha
On Wed, Feb 9, 2011 at 11:31 AM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:
> On 9/02/2011 4:48 PM, 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
>
>
> I can see nothing relevant on p62 of the 4.5 manual. When giving references
> to literature that exists in multiple versions, please be very precise.
> Giving details such as the manual version number, page number, equation
> number and description of the relationship described in the equation will
> make it much more likely that someone will (want to) (be able to) help you.
>
> Mark
>
>
>
> 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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>>
>>
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>
>
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