On 12/25/19 11:14 PM, Najamuddin Memon wrote:
It is not about to select numbers in drop down menu. You should write atom
no of protein and ligand. For example your chain a is protein having 2000
atoms. The atom no starts from 1 till 2000 for protein. And for chain b is
your ligand and your ligand has 40 atoms it is from 2001 till 2040. You can
see these atom no in .top file.
More easily, one can identify which residues reside in loops and simply
select by residue by using make_ndx.
-Justin
On Wed, Dec 25, 2019, 8:54 PM nupur munjal <nupurmun...@gmail.com> wrote:
Hi,
i am trying to make the index file without loops and termini and using the
option protein and ligand that is 1 and 13 but the index file is formed
with the same as it is formed from the whole system.
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Kind Regards
Nupur Munjal
PhD Scholar (Bioinformatics)
Department of Biotechnology & Bioinformatics
Jaypee University of Information Technology
Waknaghat, Solan,India
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