Dear David,
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?
Regards,
Olena
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 27 January 2012 20:58
To: AMBER Mailing List
Subject: Re: [AMBER] makeDIST_RST command problem
On Fri, Jan 27, 2012, Olena Dobrovolska wrote:
>
> Thanks for your advice. I decided to not change the map.DG-AMBER file
> (since it is AMBER file and it requires a superuser password).
(Plan A)
Make a copy of this file in your working directory, point makeDIST_RST to that
copy. OR:
> tried to convert H to HN in both .pdb and .dist files.
(Plan B)
Just change H to HN in the .dist file, *not* in the .pdb file. Remember
that the map file is converting what is in the .dist file to atom names
in the .pdb file. If you don't want to change the default map file, you
need to understand what conversions are being made, and prepare your files
accordingly.
...dac
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Received on Mon Jan 30 2012 - 09:30:02 PST
