[gmx-users] Parameters for PB calculation with Delphi from Gromacs data

[Ran Friedman]

Hi,

The PARSE parameters were developed in order to reproduce the hydration 
free energies in PB calculations, while charges taken from different FF 
are parametrised by MD or MC. Therefore, I tend to use both the VdW 
radii and the charges taken from PARSE. However, check the literature - 
many people have used FF parameters in their calculations.

Ran.

Marco Ceruso wrote:

>Hi;
>If you use Delphi use the PARSE vdw radii set (J. Phys. Chem. 98, 1978-1988
>(1994)). For the charges you can keep the OPLS-AA charges.
>Marco  
>  
>
>>-----Original Message-----
>>From: gmx-users-bounces at gromacs.org 
>>[mailto:gmx-users-bounces at gromacs.org] On Behalf Of Marc Baaden
>>Sent: Sunday, October 10, 2004 4:49 PM
>>To: gmx-users at gromacs.org
>>Subject: [gmx-users] Parameters for PB calculation with 
>>Delphi from Gromacs data
>>
>>
>>Hi,
>>
>>I am currently carrying out some Poisson-Boltzmann 
>>calculations with Delphi, on the basis of MD snapshots 
>>obtained with Gromacs. I wonder what parameter set (charges & 
>>radii) would be appropriate for Delphi.
>>Should one "simply" take the precise charges as used in the 
>>MD simulation, and eventually the VDW-parameter derived 
>>atomic radii, or is there some other magic involved to obtain 
>>reasonable results ?
>>
>>What are people's experience, and would users be willing to 
>>share their favorite parameter set ?
>>
>>In particular I wonder whether one would need to have 
>>different specific Delphi parameters depening on the 
>>forcefield used (ffgmx vs ffG43xx vs
>>oplsaa) ?
>>
>>Or maybe it is more appropriate to use MEAD, as some Gromacs 
>>tools allow to write corresponding input structures ?
>>
>>Any clarification or (Gromacs related/specific) litterature 
>>reference is welcome.
>>
>>Thanks in advance,
>>  Marc
>>
>>--
>> Dr. Marc Baaden  - Institut de Biologie Physico-Chimique, Paris
>> mailto:baaden at smplinux.de      -      http://www.marc-baaden.de
>> FAX: +49 697912 39550  -  Tel: +33 15841 5176 ou +33 609 843217
>>
>>
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>>    
>>
>
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-- 
------------------------------------------------------
Ran Friedman
Laser Laboratory for Fast Reactions in Biology
Department of Biochemistry
Faculty of Life Sciences
Tel-Aviv University
Tel. +972-3-6409824
Fax. +972-3-6409875
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