Re: [AMBER] question about bond command in tleap

From: Matias Machado <>
Date: Wed, 28 Aug 2019 18:33:44 -0300 (UYT)

Dear Rui,

No, this information is lost, and even if you have it, the command bond doesn't allow it in the selection syntax... So, you have to use its residue index, e.i. its number according to an index that starts from 1 (first residue in the system) to N (last residue in the system). Don't get confused by the residue number in the PDB file, which stands for the biological sequence and hence may not start from 1, even if it is the first residue in the file... (yeah that seems a tongue twister!)

The simplest way to get the residue index is processing the PDB for AMBER simulation:

pdb4amber -i your.pdb -o your_processed.pdb

then at the shell execute,

cat your_processed_sslink

Those are the expected CYX pairs numbered according to the new index that AMBER will use in the prmtop.

Beware! It may not work if Cysteine residues are too far away. Then you will have to do it "manualy" by visual inspection of the created topology and coordinate files. Anyway, visually checking your system is always a good practice before any simulation...



Researcher at Biomolecular Simulations Lab.
Institut Pasteur de Montevideo | Uruguay

----- Mensaje original -----
De: "Rui Chen" <>
Para: "AMBER Mailing List" <>
Enviados: MiƩrcoles, 28 de Agosto 2019 17:47:11
Asunto: [AMBER] question about bond command in tleap


My target protein is a homodimer, I'd like to use bond command in leap to
connect the CYS residues. Is there a way to specify chain A and chain B,
because they have the same residue numbers.

Looking forward to hearing from you.

Best regards,
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Received on Wed Aug 28 2019 - 15:00:02 PDT
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