Hi;;
When u convert ur Full_Mini.rst to Full_Mini.pdb and open it with Maestro
or LigPlot or Poseview u will get name and code of prominent residues which
are interacting with the ligand (please delete water and ions as these
makes ur file heavy for visualisation programmes).
Now suppose in com_solvated.pdb ur ligand is denoted by X1 and ur prominent
residues interactions are m1,m2,m3,m4
In that case the print option looks like:
idecomp=1, print_res="X1; m1; m2; m3; m4",
Enjoy MD
On Sun, Apr 6, 2014 at 6:07 AM, Arunima Shilpi <writetoash28.gmail.com>wrote:
> Dear Sir,
>
> Many many thanks for your response. I just have one query is here in
> print_res I have to mention the residue number for ligand as well as
> protein residue along the active site. I did not get which residues
> should I mention over here.
>
> Looking for your reply
>
>
> Regards
>
> Arunima
>
> use this input
>
> Input file for running PB and GB in serial
> &general
> startframe=1, endframe=5000, interval=5,keep_file=0, (please amend frames
> accordingly)
> /
> &gb
> igb=5,saltcon=0.15,
> /
> &decomp
> idecomp=1, print_res="561;72;15;219;184;114;110;113;115;116", (yellow
> highlighted is the ligand number)
> dec_verbose=1,csv_format=0,
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--
Thanks & Regards;
Soumendranath Bhakat
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Received on Sun Apr 06 2014 - 05:00:02 PDT
