Yes.This are my actual files. Since I am working with AMBER for the first time, I followed manual and gave a names as it is in the manual.
Olena
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 30 January 2012 23:37
To: AMBER Mailing List
Subject: Re: [AMBER] makeDIST_RST command problem
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 Tue Jan 31 2012 - 01:30:03 PST
