HI,
As I have replied to the previous thread, systems with metal ions cannot be directly used with antechamber. I have already provided you with the frcmod and prepi files which you can directly use in leap but remember you must rename your residue name and atom names in HEME to match in that in the frcmod and prepi file.
Best Regards
[photo]
Elvis Martis
Ph.D. Student (Computational Chemistry)
at Bombay College of Pharmacy
A Kalina, Santacruz [E], Mumbai 400098, INDIA
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________________________________
From: Rana Rehan Khalid <rrkhalid.umich.edu>
Sent: 29 June 2017 04:07:12
To: AMBER Mailing List
Subject: [AMBER] antechamber
hi Everyone
i used antechamber for my heme fe--o2 ligand it show this error and mol2
not formed for heme-fe----O2. i also sending you the leap.log kindly tell
me where i am wrong
Running: /home/rehan/Downloads/amber16/bin/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
For atom[26]:O01, the best APS is not zero, bonds involved by this atom are
frozen
For atom[45]:Fe, the best APS is not zero, bonds involved by this atom are
frozen
The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic
double)Error: cannot run "/home/rehan/Downloads/amber16/bin/bondtype -j
full -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit
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Received on Wed Jun 28 2017 - 20:30:03 PDT
