On Mon, Jan 30, 2012, Olena Dobrovolska wrote:
> I read carefully your advice and applied plan B: changed H to HN in
> .dist file only. My .pdb file contains H. It gives again an error
> messsage:
> makeDIST_RST -upb 16b_1_12_2.dist -pdb gcg_b.amb.pdb -rst RST.dist
> # makeDIST_RST
> Currently configured for up to 5000 atoms
> Using MAP file /usr/local/amber9/dat/map.DG-AMBER
> ERROR atom (HB1) not in residue (26) : 26 ALA HN 26 ALA QB 3.42
>
> Now it can't convert QB ALA, right? File map.DG-AMBER should convert QB to HB1, HB2, HB3 and the rest atom names. What else could be wrong in my files now?
>
Are you sure your pdb file has an HB1 atom in residue 26?
I'm actually kind of confused, since the "gcg_b.amb.pdb" from the Amber
tutorials contains DNA, not protein. You may have to post your actual files.
....dac
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Received on Mon Jan 30 2012 - 15:00:04 PST
