[AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc

From: Sharon D. Morris <sharondm.aims.amrita.edu>
Date: Sat, 22 Apr 2017 14:30:17 +0530 (IST)

Sir,

I have a problem generating the prmtop and inpcrd file of protein-ligand complex of my interest, with Zn atom using Amber 12. prmtop and inpcrd files of protein without the ligand was generated without errors. We have used frcmod.zinc and znb.lib files from http://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy-atom-cada-approach to include zinc in the library. When trying to create the files, errors like missing bond, angle, torsion parameters for zinc atom arise. Kindly help us to generate the prmtop and inpcrd files of protein-ligand complex containing zinc. We have attached the screenshots showing this error for your reference. 




-- 
Regards, 
Sharon D'Morris, 
JRF 
Amrita Center for Nanosciences and Molecular Medicine(ACNSMM) 
Amrita Institute of Medical sciences, 
AIMS-Ponekkara (P.O) 
Kochi-682041

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Received on Sat Apr 22 2017 - 02:30:03 PDT
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