On 12/02/2011 1:51 AM, Justin A. Lemkul wrote:
najwa drici wrote:
hi all
I would like to extract my protein structure with the first hydration
shell around the active site which contains an ion from counfout.gro.
Is there any program script able to do this?
Not in one step, no. You could:
1. Use make_ndx to create an index group that defines your active site.
2. Use g_dist -dist to determine which water molecules (based on the
atoms listed) are within a defined distance from the active site
residues.
3. Make another index group that contains protein + the waters
identified in step 2.
Or g_select to do some/all of 1-3.
Mark
4. Extract those coordinates using trjconv and the index group created
in step 3.
-Justin
Cordially DRICI nedjoua
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