Re: [AMBER] tleap error

From: David A Case <>
Date: Fri, 8 Nov 2019 08:25:11 -0500

On Fri, Nov 08, 2019, MYRIAN TORRES RICO wrote:
>I have looking for about this error and it seems that a problem with
>the connects in my ligand in the pdb,

Try removing the CONECT cards for the PDB that you feed to tleap. If
there are missing covalent bonds, add them yourself via the "bond"

You didn't say where these PDB files came from. But in general,
CONECT records in PDB files are notorious for being unreliable. The
Units (libraries) you have created for LEaP know where all the bonds are
supposed to be, so CONECT records should not be needed.

Also: some software will use duplicate CONECT records to indicate a
double bond. But tleap doesn't understand this convention, and so
treats that as a error.


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Received on Fri Nov 08 2019 - 05:30:03 PST
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