[AMBER] Error in prmtop and inpcrd atom

From: shivangi agarwal <shiviagarwalpharma.gmail.com>
Date: Wed, 3 Jul 2019 22:36:19 +0530

While generating prmtop and inpcrd of the complex (protein + ligand)
containing zinc atom, I am getting error as :

*For atom: .R<ZN 260>.A<ZN 1> Could not find type: Zn2+Parameter file was
not saved.*
The commands while I have followed are as:

*antechamber -i ligand.pdb -fi pdb -o ligand.mol2 -fo mol2 -c bcc -s
2parmchk -i ligand.mol2 -f mol2 -o ligand.frcmodtleapsource
leaprc.ff99SBsource leaprc.gaffLIG=loadmol2 ligand.mol2listcheck
LIGloadamberparams ligand.frcmodsaveoff LIG ligand.libsaveamberparm LIG
ligand.prmtop ligand.inpcrdquittleap -s -f Zn.intleapsource
leaprc.ff99SBsource leaprc.gaffloadamberparams ligand.frcmodloadoff
atomic_ions.libloadoff ligand.libcomplex =loadpdb rec_lig.pdbsaveamberparm
complex rec_lig.prmtop rec_lig.inpcrdsavepdb complex rec_lig.pdb*

I am attaching rec_lig.pdb, Zn.in, ligand.pdb, ligand.frcmod, ligand.mol2,
ligand.lib, ligand.prmtop, ligand.inpcrd file and atomic_ions.lib file for
your reference.
Kindly refer these files and suggest me a possible way to come out of this

Thanks and regards
Shivangi Agarwal

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Received on Wed Jul 03 2019 - 10:30:02 PDT
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