[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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