Re: [AMBER] Error while running tleap for protein-RNA complex

From: David A Case <>
Date: Mon, 11 May 2015 07:55:17 -0400

On Mon, May 11, 2015, Shreeramesh wrote:
> WARNING: There is a bond of 7.165783 angstroms between:
> ------- .R<LEU 358>.A<C 18> and .R<LYS 359>.A<N 1>

You'll have to examine your starting structure to figure out the origin of
warnings like these...are there missing residues in your protein?

> Could not find bond parameter for: SH - SH

This is probably because you have CYS residues in your protein that should be
CYX. A simple approach is to use the pdb4amber script on your input pdb file
before loading it into tleap.

> FATAL: Atom .R<RG5 170>.A<P 33> does not have a type.

The 5' residues in Amber do not have a terminal phosphate, but this group is
apparently present in your input pdb file. There is hence a mismatch between
the library and your input pdb, which needs to be resolved, either by removing
the phosphate group from the pdb file, or by generating an appropriate library
[There may(?) already be such a unit in the RED database. In any event, some
enterprising developer should make it easier to handle these 5' phosphates,
since they come up reasonably often.]


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Received on Mon May 11 2015 - 05:00:03 PDT
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