Re: [AMBER] To build a single covalent bond in a protein-ligand complex using AMBER18.

From: David A Case <>
Date: Mon, 19 Jul 2021 12:15:39 -0400

On Mon, Jul 19, 2021, PRIYANKA PUROHIT wrote:

>Thank you Elvis for your response. However, the protein complex I am using
>contains a protein as the receptor and a small peptide as the ligand. Both
>are different units but connected by a single bond.

There is understandable confusion about what a UNIT is in Amber. Basically,
you have to eventually combine all pieces of your system into a single UNIT,
so the saveAmberParm can create a prmtop file.

tleap has commands to combine small units into bigger ones, but I often find
that approach to be confusing. My (personal) recommendation is this:

1. prepare a PDB with all components in it (include TER cards if needed to
separate different chains, or ligands from protein, etc.)

2. use loadPdb to slurp in this file into a single, comprehensive unit, e.g.
       x = loadPdb <pdf-file-name>

3. You can then use the desc command to see how leap has numbered
everything, and the "bond" command to add whatever bonds you want.

Either with this method, or some other way, you indeed have to combine
protein and peptide into a single UNIT before using the bond command to
connect the two.

...goodl luck....dac

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Received on Mon Jul 19 2021 - 09:30:02 PDT
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