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

[Mark Abraham]

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
>>
>>
>