[AMBER] Problem in creating topology and coordinate files

From: Mustafa Alhaji Isa <mustafaisa.unimaid.edu.ng>
Date: Sun, 11 Jun 2017 11:19:59 +0530

I want to create topology and coordinate files of protein-ligand
complex. but when I load the complex it display the below commands and
subsequently failed the create the files

Created a new atom named: HD2 within residue: .R<ASP 80>
Created a new atom named: HD1 within residue: .R<HIE 137>
Created a new atom named: HD1 within residue: .R<HIE 193>
Created a new atom named: HD1 within residue: .R<HIE 408>
Created a new atom named: HD1 within residue: .R<HIE 410>
  total atoms in file: 6041
  Leap added 10 missing atoms according to residue templates:
       10 H / lone pairs
  The file contained 5 atoms not in residue templates

-- 
Warm regards
Mustafa Alhaji Isa
PhD Scholar
Bioinformatics and Computational BIology Lab,
Department of Biotechnology,
School of Engineering and Technology
Sharda University
Greater Noida, Delhi, India
Mob No.: +918800621829
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Received on Sat Jun 10 2017 - 23:00:02 PDT