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
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: Monday, April 24, 2017 10:48 AM
To: AMBER Mailing List <amber.ambermd.org>
Cc: Anu Rohit Melge <anurm19924.aims.amrita.edu>
Subject: Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc
Hi,
I have attached leap.log, frcmod.zinc and znb.lib for your kind reference.
----- 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: Saturday, April 22, 2017 6:23:17 PM
Subject: Re: [AMBER] failed to generate parameter and topology file for protein-ligand complex containing zinc
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
--
Regards,
Sharon D'Morris,
JRF
Amrita Center for Nanosciences and Molecular Medicine(ACNSMM)
Amrita Institute of Medical sciences,
AIMS-Ponekkara (P.O)
Kochi-682041
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 24 2017 - 00:30:02 PDT
