Re: [AMBER] There is a bond of 8.882728 angstroms between: [Blank]

From: David Case <>
Date: Wed, 10 Jul 2019 16:30:20 +0000

On Tue, Jul 09, 2019, Anthony Bogetti wrote:

>Thank you both for the help. It turns out there are missing residues from
>the crystal structure that we didn't see when setting up the initial model.

Another suggestion to avoid this problem: always use pdb4amber to
process PDB files before submitting them to tleap. pdb4amber will
identify gaps in the structure.

That said: the tleap output should not have a <blank> when identifying
the long "bond". Scott: can you take a look at this?


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Received on Wed Jul 10 2019 - 10:00:02 PDT
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