Dear Sir,
Can you please tell me how to analyse H-bonds if a PDB file has both
protein and ligand residues. I am not getting which command should I use
for general case. Like, I have total 127 residues out of which 124 belongs
to protein and 2 residues of ligand and one is water molecule.
I am using the following hbond_analysis.ptraj file :
ptrajin xyz.min.crd
donor mask :1-124 :1-124
acceptor mask :1-124.N
donor print
acceptor print
hbond distance 3.5 angle 120.0
Please tell me some general commands so as to consider all residues because
I dont want to specify any residues or atoms.
Thanks in advance...
--
Swati Adlakha
M.tech Bioinformatics
Indian Institute Of Information Technology,
Allahabad, U.P.
INDIA
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Received on Tue Feb 28 2012 - 06:00:02 PST
