I believe that ignoring hydrogen atoms is the default behaviour of any
software calculating ASA values. Normally the VdW radii values of the
heavy atoms already include the hydrogens implicitly.
If your input structure has hydrogens and they were included in the
calculation it would result in over-estimating the ASA values. I'm not
familiar with AREAIMOL but I guess it must behave in a similar way.
Jose
On 28/07/14 14:02, Harry Mark Greenblatt wrote:
BS"D
Dear All,
I understood from the areaimol documentation that hydrogens are not
included as one of the default atoms. But one can add atoms, and so I
added an "ATOM" line for hydrogen. The program quite happily accepted
my input line, but later on stated explicitly that it was ignoring the
hydrogens. Is there no way to include hydrogens?
Thanks
Harry
-------------------------------------------------------------------------
Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology
Weizmann Institute of SciencePhone:972-8-934-3625
234 Herzl St. Facsimile: 972-8-934-4159
Rehovot, 76100
Israel
[email protected] <mailto:[email protected]>
