AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: Ilyas Yildirim (yildirim_at_pas.rochester.edu)
Date: Wed Jul 02 2008 - 04:58:05 CDT

I had similar problems when I tried to do simulated annealing. The
tutorial is very useful to guide someone on how to apply NMR restraints to
sander. There are two things that someone has to be careful.

1. The .pdb file that is used in makeANG_RST and makeDIST_RST has to have
exactly the same atom naming as prmtop file. In order to get a .pdb file
that can be used for this purpose, make sure that you do the following:

ambpdb -aatm -p prmtop <inpcrd> structure.aatm.pdb

You can use structure.aatm.pdb in creating the RST files.

2. You will need to modify the map.DG-AMBER file, according to your
new/modified residues. Try to understand what/how the atoms are defined.
This is very important. Just copy-pasting the previous residue
information might make things confusing. Try to write every line
carefully. If you are going to use torsional restraints, you will need to
play with tordef.lib file.

Good luck,

On Wed, 2 Jul 2008 teresa.ierano_at_unina.it wrote:

> 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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-- 
  Ilyas Yildirim
  ---------------------------------------------------------------
  = Department of Physics        -                              =
  = University of Rochester      -                              =
  = 585-275-6766 (office)        - 585-267-5644 (home)          =
  = http://www.pas.rochester.edu/~yildirim/                     =
  ---------------------------------------------------------------

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