[gmx-users] extracting a structure from confout.gro file

Justin A. Lemkul jalemkul at vt.edu
Fri Feb 11 15:51:33 CET 2011

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.

4. Extract those coordinates using trjconv and the index group created in step 3.


> Cordially DRICI nedjoua


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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