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

[Justin A. Lemkul]

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.

-Justin

> Cordially DRICI nedjoua
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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