AMBER Archive (2008)

Subject: Re: AMBER: NMR refinement

From: teresa.ierano_at_unina.it
Date: Thu Jul 03 2008 - 04:37:02 CDT

I tried to modify carefully each line of map.DG-AMBER file according
to my file.amb.pdb and now it works!!!
Now I'm ready for the MD!
Thank you for your precious advice!

Quoting Ilyas Yildirim <yildirim_at_pas.rochester.edu>:

> 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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