AMBER Archive (2004)

Subject: Re: AMBER: protein-carbohydrate complex

From: Bill Ross (
Date: Thu Apr 22 2004 - 17:39:16 CDT

> I divided into each protein and carbohydrate pdb file
> from whole complex pdb file.

The only reason to do this would be to build prepin files
for any residues missing from the standard database. In which
case I expect that the residue would be separated from all
other residues, tho I don't know antechamber procedures.

> I created prep file for my carbo using antechamber with charges=0.
> (because I want to use resp charges from Woods' parameters)

If you are using Woods' residues, there should be no reason to
build a prepin. Prepin's are made for each new residue type.

> In xleap, I loaded carbo prep file and loaded protein pdb file.
> And then I combined them using combine command.

No reason to do this - basic procedure is

1. load all residue templates and parameter/frcmod files
2. load pdb with whole complex.

If all residues are defined correctly, all bonds should be drawn.

It may be worthwhile to study the examples.

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