[phenixbb] ReadySet & phenix.refine problem: NAG-Asn with hydrogen atoms

Nigel Moriarty nwmoriarty at lbl.gov
Mon Apr 29 16:36:59 PDT 2013

Can you send me the ASN-NAG PDB file?

On Mon, Apr 29, 2013 at 4:01 PM, Zhijie Li <zhijie.li at utoronto.ca> wrote:

> **
> Hello,
> I am refining my structure with hydrogen atoms on (phenix 1.8.2-1309). The
> protein contains two Asn-linked GlcNAc. I noticed two problems with respect
> to the NAG-Asn linkage in the presence of hydrogen atoms:
> 1) After running ReadySet (to add hydrogen to the PDB *ab initio*), the
> H1 on the NAG is pointing to the amino group of Asn, ie, the NAG seems to
> be interpreted as in its alpha anomer instead of beta (should be GlcNAc
> beta1,N-Asn). This is not really a problem as it doesn't seem to affect the
> refinement.
> 2) The H21 in Asn is correctly removed by ReadySet, leaving only H22.
> However, if I send this PDB to phenix.refine, the refinement will fail
> almost instantly complaining that H22 of the Asn has an unknown nonbonded
> energy type symbol. But if I simply change the atom name of H22 to H21, the
> refinement will proceed to completion with no problem, only leaving an
> H21 at the position where H22 should be.
> I was not sure what caused this error. So I trimmed my PDBs down to the
> Asn and NAG only, and fed the small PDB to ReadySet and phenix.refine (with
> an eff file indicating the NAG-Asn linkage) and got the same behavior: H22
> on Asn - error; H21 on Asn - OK.
>  I hope someone can look into this. Thanks in advance.
> Zhijie
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Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709     Email : NWMoriarty at LBL.gov
Fax   : 510-486-5909       Web  : CCI.LBL.gov
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