[gmx-users] Re: Force field parameters for GROMACS

[David van der Spoel]

On Wed, 6 Feb 2002 Brian.Smith at wehi.edu.au wrote:
>
>The GROMACS 3.0 force field is based on the GROMOS-87 force field 
>(apparently, Chapter 4 , p47 of the GROMACS manual). The problem is that 
>the GROMOS-87 force field is not described anywhere in the generally 
>available literature - if you consider the GROMOS-87 manual to be 
>generally not available.
>
>So my questions,
>1) Is the GROMACS 3.0 force field described anywhere else (in 
>particular, the details of how each inividual parameter was determined).
There is an old reference:
@Article{Hermans84,
  author = 	 {J. Hermans and H. J. C. Berendsen and W. F. van
                  Gunsteren and J. P. M. Postma},
  title = 	 {A consistent Empirical Potential for Water-Protein
                  interactions},
  journal = 	 {Biopolymers},
  year = 	 1984,
  volume =	 23,
  pages =	 {1513-1518}
}
which doesn't cover it all...

>2) In particular, how were the parameters for the amino acids 
>determined? (I've seen in the literature of how parameters have been 
>determined for things like water or DMSO, but not for amino acids).
Basically they were copied from an even older forcefield, and then the 1-4 
(reduced) LJ interactions were adapted until a test protein was more or 
less stable..

>I'm trying to determine parameters for non-standard amino acids, and 
>would like to keep as close as possible to the original detemination 
>procedure.
Try to use analogous groups from other amino acids. There is no "standard" 
way to determine charges (like in Amber) or LJ parameters.

Groeten, David.
________________________________________________________________________
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel
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