Hi,
By default the 'secstruct' command looks for Amber default backbone
atom names. If you are using a topology where these names are
different, you will have to change the backbone atom names accordingly
(with [namen <N name>], [nameh <H name>], [namec <C name>], and/or
[nameo <O name>]). For example, if you are using a CHARMM topology,
the backbone amide hydrogen is named 'HN', not 'H'. You can change
this by adding 'nameh HN' to your 'secstruct' commands.
Hope this helps,
-Dan
On Tue, May 20, 2014 at 2:00 PM, Marlet Martinez <marletm8.gmail.com> wrote:
> Dear Amber users,
>
> I have used Cpptraj to calculate the secondary structure of my protein
> however the output files: dssp.dat and dssp.dat.sum appear just with "0s"..
>
> When I look at the .log file I got this message:
>
>> Warning: Not all BB atoms found for 268 residues: LYS:1 ...
>> Info: This is expected for Proline and terminal/non-standard residues.
>> Info: Expected BB atom names: N=[N ] H=[H ] C=[C ] O=[O ]
>> Info: Re-run with action debug level >= 1 to see which residues are
> missing atoms
>
> Does anyone knows how to fix this problem?
>
>
> Thanks in advance
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Tue May 20 2014 - 14:00:04 PDT
