Open your com_solvated.pdb file. Identify the mask which denote the ligand.
Suppose residue mask is 556 and if you open the minimized pdb you can
identify some crucial residues such as X1, X2 take out their atom mask.
In the print residue put like this "556,X1,X2".
It will work.
All the best!!
On Tue, May 27, 2014 at 12:21 PM, Jason Swails <jason.swails.gmail.com>wrote:
> On Mon, May 26, 2014 at 11:52 PM, Arunima Shilpi <writetoash28.gmail.com
> >wrote:
>
> > Dear Sir
> > I have one query. While we execute MMGBSA/MMPBSA using the following file
> >
> > Can you tell me how do we make protein-ligand pair for print residue. I
> am
> > sending you the minimized file for protein-ligand complex. Kindly guide
> me
> > with the residue paring.
> >
> >
> >
> > Input file for running PB and GB in serial
> > &general
> > startframe=1, endframe=5000, interval=50,keep_file=0,
> > /
> > &gb
> > igb=5,saltcon=0.15,
> > /
> > &decomp
> > idecomp=1,
> > print_res="",
> > dec_verbose=1,csv_format=0,
> >
>
> Your print_res variable is empty (and you never terminated the &decomp
> namelist). See the definition of print_res in the Amber manual -- this
> variable is responsible for controlling which residue pairs will have their
> interactions printed to the output file.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Thanks & Regards;
Soumendranath Bhakat
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Received on Tue May 27 2014 - 04:30:02 PDT
