HI,
Can give send your leap.log?
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in
Skype. adrian_elvis12
-----Original Message-----
From: Sharon D. Morris [mailto:sharondm.aims.amrita.edu]
Sent: Saturday, April 22, 2017 2:30 PM
To: amber.ambermd.org
Cc: Anu Rohit Melge <anurm19924.aims.amrita.edu>
Subject: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc
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 - 06:00:04 PDT
