Re: [AMBER] Problem of loading complex

From: David A Case <>
Date: Fri, 8 Dec 2017 20:51:32 -0500

On Sat, Dec 09, 2017, Mustafa Alhaji Isa wrote:

> The 419 is the ligand
> -- residue 419: duplicate [ C] atoms (total 30)
> -- residue 419: duplicate [ H] atoms (total 2)
> -- residue 419: duplicate [ N] atoms (total 4)
> -- residue 419: duplicate [ O] atoms (total 3)

Atom names within a residue must be unique. Looks like all your carbons
are named "C", etc. (Also looks like you are missing most sure
to check that. You'll have to add hydrogens before make the library mentioned
in the next paragraph.)

Even if the atom names were made to be unique, you can't just pass a pdb file
with an arbitrary ligand to tleap. You have to create an Amber library for
that first. See tutorial B4 for an example of how this is done.


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Received on Fri Dec 08 2017 - 18:00:02 PST
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