[gmx-users] solvation

[David van der Spoel]

On Tue, 2003-12-02 at 20:49, sadhna wrote:
> hi ,
>     I would like to know how the surface.dat file in the gromacs has been
> generated. What is the united atom vdw radii used for calculation of
> surface of each residue and what is the conformation(dihedrals of backbone
> and side chain) of the residues.
> 
I'm sorry to say that I don't know the history of the file, but since it
is used in DSSP I assume these numbers were computed with the DSSP SASA
algorithm from individual amino acids.

> thanks
> 
> sadhna
> 
> Sadhna Joshi
> Research Scholar
> Dept of Chemical Engg
> Indian Institute of Technology,Powai
> Mumbai-400076
> India
> 
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assist. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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