Say for example you ligand mask is 905 and your crucial amino acid residues
are 902 and 903. Then in print residue put like this "905,902,903"
Thats it.
Enjoy
On Tue, May 27, 2014 at 1:13 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
>
>
--
Thanks & Regards;
Soumendranath Bhakat
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue May 27 2014 - 04:30:02 PDT
