Re: [AMBER] Defining new atoms in AMBER

From: David A Case <>
Date: Fri, 3 Jul 2020 09:41:54 -0400

On Thu, Jul 02, 2020, Kolattukudy P. Santo wrote:

>I am trying to model an octahedral zinc coordination model - with four
>water occupying the coordination cites modeled as in the 'bonded' model and
>the rest two cites as dummy atoms available for ligands as in the cationic
>dummy atom (CADA)model.
>I defined oxygens (DO), hydrogens(DH), dummy atoms(DZ) and the central
>zinc(ZO) as new atoms in xleap and created lib files. The frcmod files
>created with TIP3P parameters for water and CADA parameters for Zinc and
>Loading PDB file: ./zoct.pdb
> Added missing heavy atom: .R<ZOB 5>.A<DO4 1>
> Added missing heavy atom: .R<ZOB 2>.A<DO1 1>
> Added missing heavy atom: .R<ZOB 3>.A<DO2 1>
> Added missing heavy atom: .R<ZOB 13>.A<DH8 1>

This means that there is a atom named DO4 in the ZOB residue in the PDB
file, but there is no such atom in your library file. You have to make
sure that residue and atom names match.

If you can't figure it out, post the actual files for a small example;
just describing in words what you tried to do is often fruitless: people
need to be able to reproduce the error.


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Received on Fri Jul 03 2020 - 07:00:04 PDT
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