My problem is that I have a oligosaccharidic sequence constitued by
glucose,galactose,
heptoses, aminoarabinose, rhamnose and Kdo (2-cheto-3-deoxy-manno
octulosonic acid)!
I would like to perform the NMR refinement on my molecule and I
started by creating a
topology and coordinate file through xleap and then I create a pdb
file containing the
topology and coordinates informations (oligo.amb.pdb).
Then I went to the next step and I tried to create a 7col.dist file
following the
template giving by the tutorial for DNA:
2 MEL H4 2 MEL H6 4.0.
2 MEL H3A 2 MEL H3E 4.0.
2 MEL H3A 2 MEL H4 4.0.
3 MOT H1 3 MOT H2 4.0.
3 MOT H1 3 MOT H5 4.0.
3 MOT H1 12 OGB H61 4.0.
...
(N.B. MEL and MOT are my residues name recognised by xleap)
Then I typed:
makeDIST_RST -upb 7col.dist -pdb oligo.amb.pdb -rst RST.DIST
and it gave me a error message:
ERROR no map function for H6 MEL :data= 2 MEL H4 2 MEL H6
4.0.
And it creates a RST.dist file empty.
Then I tried to add my fragments to the map.DG-AMBER file used by
default, just by
listing the atom contained in each residue of my oligosaccharide:
residue MEL
MAPPING H1 = H1
MAPPING C1 = C1
MAPPING H4 = H4
MAPPING H6 = H6
...
residue MOT
MAPPING ...
...
This time it gives the same error message but for a different NOE contact:
ERROR no map function for H61 OGB :data= 3 MOT H1 12 OGB
H61 4.0
and this time it gives a RST.dist file compiled until the NOE contact
for which it gives the error (that is to say until line 5 of the
7col.dist exemple file that I've reported above)!
So I guess I have to modify MAP file in order to create the RST.dist
file but I don't know how (especially for methylen and methyl protons)!
Thanks for your help!
Best regards,
teresa ierano'
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Received on Sun Jul 06 2008 - 06:07:06 PDT
