[gmx-users] list of protein parameters/ properties

[Tsjerk Wassenaar]

Hi Gaurav,

Look in the Gromacs manual where all the programs are explained. This gives
plenty of ways to describe a protein (radius of gyration, dipole, hydrogen
bonds, secondary structure, dipole, solvent accessible surface, etc.).

Cheers,

Tsjerk

On 11/16/05, gaurav gupta <gaurav.cgupta at gmail.com> wrote:
>
>
> hi,
>  i am a recent user of gromacs and was introduced to it by the person who
> was using it for organic mol modelling.
> i am working on protein molecule and interested in finding the properties
> related to the structure of a protein mol..like dielectric constant,
> radius,pKa ,surface tension ..etc..I would like to know the list of
> descriptors related to protein which can be calculated using PDB file..i
> would appreciate if the help is given along with an example.
>  my research topic is totally depend on this calculation so i need a
> software which can help m to deal with proteins.
> thank you waiting for an early response
>
> --
> "gaurav gupta"
> M.TECH( B.P.T),
> U.I.C.T, Matunga,Mumbai
>
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--

Tsjerk A. Wassenaar, M.Sc.
Groningen Biomolecular Sciences and Biotechnology Institute (GBB)
Dept. of Biophysical Chemistry
University of Groningen
Nijenborgh 4
9747AG Groningen, The Netherlands
+31 50 363 4336
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