[phenixbb] reduce and ready_set problem
Nigel W Moriarty
NWMoriarty at lbl.gov
Mon Jan 11 09:29:24 PST 2010
Jianghai
Can you send me the the input PDB directly?
Nigel
On 1/6/10 12:52 PM, Jianghai Zhu wrote:
> Hi,
>
> I believe I have reported this bug before, but it is not fixed in the phenix.reduce and phenix.ready_set yet. The problem is the hydrogens added by reduce when there is a glycan. Here is the error message.
>
> Number of atoms with unknown nonbonded energy type symbols: 12
> "ATOM 8332 HD22 ASN B 99 .*. H "
> "ATOM 11820 HD22 ASN B 320 .*. H "
> "ATOM 12615 HD22 ASN B 371 .*. H "
> "ATOM 14058 HO4 NAG B3320 .*. H "
> "ATOM 14086 HO4 NAG B3321 .*. H "
> "ATOM 14136 HO4 NAG B3371 .*. H "
> "ATOM 22458 HD22 ASN D 99 .*. H "
> "ATOM 25955 HD22 ASN D 320 .*. H "
> "ATOM 26750 HD22 ASN D 371 .*. H "
> "ATOM 28256 HO4 NAG D3320 .*. H "
> ... (remaining 2 not shown)
> ...
>
>
>
> Sorry: Fatal problems interpreting PDB file:
> Number of atoms with unknown nonbonded energy type symbols: 12
> Please edit the PDB file to resolve the problems and/or supply a
> CIF file with matching restraint definitions, along with
> apply_cif_modification and apply_cif_link parameter definitions
> if necessary.
> Also note that phenix.ready_set and phenix.elbow are available
> for creating restraint definitions (CIF files).
>
>
> The hydrogen left on the N atom of the ASN is correct, but should be named as HD21 as defined in the ccp4 cif library. And the HO4 for the NAG glycan is just wrong. I have to delete all these hydrogens to get phenix.refine going.
>
> -- Jianghai
>
>
>
>
>
>
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>
>
--
Nigel W. Moriarty
Building 64R0246B, Physical Biosciences Division
Lawrence Berkeley National Laboratory
Berkeley, CA 94720-8235
Phone : 510-486-5709
Fax : 510-486-5909
Email : NWMoriarty at LBL.gov
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