Re: [AMBER] Got an error on tleap

From: David A Case <>
Date: Mon, 3 Oct 2016 07:36:49 -0400

On Mon, Oct 03, 2016, Elka Firmanda wrote:
> Loading PDB file: ./1gh0.pdb
> Added missing heavy atom: .R<MEN 234>.A<OXT 3>

This looks like you have an OXT atom in your MEN library, but that should
not be there, since this residue is in the middle of a chain.

Also, be sure there is no TER card after the MEN residue in the PDB file: it
looks like tleap is trying to start a new chain.

> ERROR: Comparing atoms
> .R<MEN 234>.A<ND2 15>,
> .R<MEN 234>.A<HE21 18>,
> .R<MEN 234>.A<HE22 19>, and
> .R<MEN 234>.A<HE23 20>
> to atoms
> .R<MEN 234>.A<ND2 15>,
> .R<ALA 1>.A<N 1>,
> .R<MEN 234>.A<HE21 18>, and
> .R<MEN 234>.A<HE22 19>
> This error may be due to faulty Connection atoms.
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 142
> !FATAL: Message: Atom named N from ALA did not match !
> !

Try building the system with ASN in place of MEN, just to eliminate other
possible sources of problems.

> There is two modified residue on the PDB (1GH0 chain A-F), CYC and MEN. I
> just followed the instruction on tutorial B5 simulating the Green
> Fluorescent Protein (

This is not really enough information: we would need more information about
the exact steps you took. I appreciate the fact that creating modified
residues is harder than it needs to be. You might want to try the R.E.D.
server: I've not used it myself, but my understanding is that it makes it
easier to do things like this. You certainly want to make sure that you don't
have an OXT atom in your MEN residue.

....good luck....dac

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Received on Mon Oct 03 2016 - 05:00:02 PDT
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