Re: [AMBER] Error in prmtop and inpcrd atom

From: David Case <>
Date: Wed, 3 Jul 2019 17:44:59 +0000

On Wed, Jul 03, 2019, shivangi agarwal wrote:

> For atom: .R<ZN 260>.A<ZN 1> Could not find type: Zn2+
>*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*

Your email program (or maybe mine?) has made it very hard to read the
above. But it looks like you are using a very old version of
AmberTools, since we have not had a "leaprc.ff99SB" in the search path
for many years. I suspect that you are never loading the parameters for
ions like zinc.

I think you are going to have to download AmberTools19, and read Chapter
3 about how force fields are loaded. You can keep your old ligand.*
files. The default approach will treat interactions between zinc and
other atoms as non-bonded ones. You'll have to see if this meets your
needs. If not, consult sections 15.7 and 15.8 in the manual, which
discusses ways to handle metals.

...good luck....dac

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Received on Wed Jul 03 2019 - 11:00:01 PDT
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