Hi David!
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). Instead I tried to convert H to HN in both .pdb and .dist files. And in .dist file even removed the signs after three letter amino acid code (like ARG+ to ARG) using sign.sed file. Again, I attached the new files. And still it gives the following message:
makeDIST_RST -upb 16b_1_12_2.dist -pdb gcg_b1.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 (H) not in residue (26) : 26 ALA HN 26 ALA QB 3.42
What else I can try to do?
Thanks
________________________________________
From: David A Case [case.biomaps.rutgers.edu]
Sent: 26 January 2012 22:34
To: AMBER Mailing List
Subject: Re: [AMBER] makeDIST_RST command problem
On Thu, Jan 26, 2012, Olena Dobrovolska wrote:
> ERROR no map function for H ALA :data= 26 ALA H 26 ALA QB 3.42
To be conservative, the makeDIST_RST program does not map atoms to themselves
by default (in order to help catch typos in your input files.) If you look
at the map.DG-AMBER file, you will see that the ALA mapping takes "HN" (in
NMR-language) to H (in Amber language).
In the old days, NMR people almost always called the amide proton "HN". This
is by now mostly out of date. But you can just edit the map file to map "H"
to "H", which should solve your problem.
[You may also find that the map file doesn't know about residues like ARG+
and GLU- (not sure, since it may be smart enough to use only the first three
characters. If so, you need to edit the 7-col file.]
...good luck....dac
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- application/octet-stream attachment: sign.sed
Received on Fri Jan 27 2012 - 06:30:02 PST
