[AMBER] Disulphide bonds

From: Gustaf Olsson <gustaf.olsson.lnu.se>
Date: Mon, 14 Dec 2020 08:54:19 +0000

Hello everyone

I just want to double check something.

I ran packmol including a peptide with a disulphide bond, using only the one peptide packmol seems to have added the correct conect record in the produced PDB file:

    CONECT 9 52

Then when I run leap with 'bond sys.2.SG go.7.SG’ and try to write top/crd files leap exits with an error:

    !FATAL: Message: 1-4: cannot add bond 14 95
    This may be caused by duplicate bond specifications;
    for example, explicit bond commands in addition to PDB conect records.

Is it safe to assume that the correct conect record in my PDB file is correctly applied in leap or is this something which should be “stripped” from the PDB and the bond created using leap.

Best regards
// Gustaf
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Received on Mon Dec 14 2020 - 01:00:02 PST
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