AMBER Archive (2008)

Subject: AMBER: NMR refinement

From: teresa.ierano_at_unina.it
Date: Wed Jul 02 2008 - 03:38:57 CDT

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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