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:
[log in to unmask]" type="cite"> 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
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Harry M. Greenblatt
Associate Staff Scientist
Dept of Structural Biology
Weizmann Institute of Science Phone: 972-8-934-3625
234 Herzl St. Facsimile: 972-8-934-4159
