Re: [AMBER] Problem with covalently bonded ligand parametrization

From: Gustavo Avelar Molina <>
Date: Sat, 23 May 2015 23:59:03 +0000

Hi, David.

Thanks for your help. I didn't managed to solve this problem yet, but I've
figured out that the protein alone works, so the problem must be associated
to the residue modification, as you said.

I've been using the tutorials B0 and B5 too.

About the protein modification... The ligand structure as well as its
atomic charges were obtained from ab initio optimization using ORCA and
CHELPG method. After that, the pdb file was obtained through conversion
using Open Babel. The mol2 file as well as the parameters for the molecule
were obtained through antechamber (except the charges, that I've replaced
by that obtained from ORCA/CHELPG), just as the Antechamber tutorial
indicates. On PyMol, I deleted the hydrogen atom linked to a sulfur atom
from a cysteine residue in the protein, as well as a whole cysteine residue
that was linked to the ligand. Then I selected the sulfur atom from the
protein and the carbon atom from the ligand, and unite them by using the
"fuse" command. The pdb file was finally saved and used as I explained



Em sáb, 23 de mai de 2015 às 13:45, David A Case <>

> On Sat, May 23, 2015, Gustavo Avelar Molina wrote:
> > I get a lot of messages like:
> > Added missing heavy atom: .R<NTRP 254>.A<O 26>
> This means that the Amber residue library for N-terminal TRP is expecting
> an
> atom named "O", but that is missing from your input PDB file. You need to
> see
> if this is expected, or if it means that something is wrong.
> >
> > At the end, I receive this message:
> >
> > Bond: Maximum coordination exceeded on .R<ACR 223>.A<H6 31>
> > -- setting atoms pert=true overrides default limits
> > ATOMS NOT BONDED: .R<ACR 196>.A<C5 12> .R<ACR 223>.A<H6 31>
> Something is surely wrong here, but we would need a lot more information
> about how how tried to make your modified residue to be of any help.
> Tutorial B5 shows an example of how to set up a simulation with a covalent
> protein modification. Make sure you understand what is going on there
> (especially since you say you are new to Amber.)
> ....regards...dac
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Received on Sat May 23 2015 - 17:00:02 PDT
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