AMBER Archive (2007)

Subject: Re: AMBER: how to modify map.DG-AMBER file?

From: A Box (boxtwin2_at_gmail.com)
Date: Tue Apr 10 2007 - 18:56:21 CDT

On 3/7/07, Seth Lilavivat <sethl_at_gatech.edu> wrote:
>
> Dear Amber Community,
>
> I am placing some restraints on a modified NA structure. I created an 8
> column
> restraint file and am trying to use makeDIST_RST to build my RST
> file. Since my
> structure contains non-standard residues, I have to modify my map.DG-AMBERfile.
>
> I'm not sure how to do this. I simply added my residues in similar
> fashion to
> the ones that were already there, but admittedly I don't know the meaning
> of
> what I was doing. Here is an example of one of the residue mappings that
> I have
> added.
>
> RESIDUE DX5
> MAPPING H8 = H8
> MAPPING H1' = H1'
> MAPPING H2' = H2'1
> MAPPING H2'1 = H2'1
> MAPPING HO'2 = HO'2
> MAPPING H3' = H3'
> MAPPING H4' = H4'
> MAPPING H5' = H5'1
> MAPPING H5'1 = H5'1
> MAPPING H5'' = H5'2
> MAPPING H5'2 = H5'2
> MAPPING Q5' = H5'1 H5'2
> MAPPING O6 = O6
> MAPPING H1 = H1
> MAPPING N1 = N1
> MAPPING N2 = N2
> MAPPING 032 = O32

It looks like you have a zore and not a capital o in this line: MAPPING
032 = O32

Try changing the first O32.

When I run makeDIST_RST I get the following error:
>
> Using MAP file /home/seth/amberfiles/map.DG-AMBER
> ERROR no map function for O32 DX5 :data= 1 DX5 O32 16 DA3 H36
> 1.75
> 1.95
>
> It is hard for me to tell what's going on because I don't know the inner
> workings of how all this works. Any help is appreciated.
>
> Thanks,
> Seth
>
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