[phenixbb] [Spam] Re: NAG-ASN link

Jianghai Zhu jzhu at cbr.med.harvard.edu
Sun Oct 7 08:54:16 PDT 2007

Hi Ralf,

I now know what happened.  When reduce adds H atoms into the pdb  
file, it finds the glycosylation bonds between NAG and ASN.  There  
are two H atoms attached to the ND2 of ASN and reduce deletes the H  
atom named HD21 and keeps HD22.  However, in the mon_lib_list.cif,  
the library wants to delete the other H atom named HD22 and keep  
HD21.  That's where this error came from.  So if I change the HD22 to  
HD21, everything is fine.  If I delete HD22, it is fine too.  I have  
a lot of glycans and it is very tedious to manually change HD22 to  
HD21 or delete HD22 one by one in the pdb file.  Could you please fix  
this?  Thanks.


Jianghai Zhu, Ph.D
CBR Institute for Biomedical Research
Department of Pathology
Harvard Medical School
200 Longwood Ave., Boston, MA 02115
Ph: 617-278-3211
Fx: 618-278-3232

On Oct 6, 2007, at 10:40 PM, Ralf W. Grosse-Kunstleve wrote:

> Hi Jianghai,
> The NAG-ASN link is defined with two modifications (in  
> mon_lib_list.cif):
> NAG-ASN  NAG      DEL-O1   .        ASN      DEL-HD22 .
>  bond_NAG-C1_=_ASN-ND2
> I haven't looked at the chemistry, but this definition suggests you
> have to remove the HD22 atom. I.e. remove the corresponding ATOM
> record from you PDB file. Note that
>    Number of atoms with unknown nonbonded energy type symbols: 1
>      "HD22 ASN A  15 "
> is formatted exactly like in the PDB file, so you can use this
> as a search pattern to find the line directly.
> Ralf
> _______________________________________________
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> phenixbb at phenix-online.org
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