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

[Jianghai Zhu]

Hi Ralf,

This doesn't work.  I removed all the H atoms from the pdb file and  
got the same error.

Jianghai

+++++++++++++++++++++++++++++++
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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