Hi,
I guess I would pay more attention to this warning in you log file
"4 unknown element"
And Secondly I would add two Na+ ions to neutralize the system before MD
Check this warning "WARNING: The unperturbed charge of the unit: -1.999001 is not zero."
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: Tuesday, May 02, 2017 5:53 PM
To: AMBER Mailing List <amber.ambermd.org>
Cc: Anu Rohit Melge <anurm19924.aims.amrita.edu>
Subject: [AMBER] Fwd: failed to generate parameter and topology file for protein-ligand complex containing zinc
Hi,
We removed the CONNECT terms from the pdb file as noted from the site:"
http://www.mayo.edu/research/labs/computer-aided-molecular-design/projects/zinc-protein-simulations-using-cationic-dummy-atom-cada-approach" and could save the protein-ligand complex parameter and topology files (.prmtop and .inpcrd). We are attaching the leap.log file along with this mail, kindly tell us whether the output is right.
----- Original Message -----
From: "Elvis Martis" <elvis.martis.bcp.edu.in>
To: "AMBER Mailing List" <amber.ambermd.org>
Cc: "Anu Rohit Melge" <anurm19924.aims.amrita.edu>
Sent: Monday, April 24, 2017 3:24:14 AM
Subject: Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc
HI,
Your Zinc seems to have an illegal name "Zn" try replacing it by "ZN" and then try again.
There are couple of other warnings in the leap.log, have a look at them carefully.
Best Regards
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
--
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 Tue May 02 2017 - 07:30:02 PDT
