Thanks a lot for your recommendation Dan, now it works.
All best
2014-05-20 22:45 GMT+02:00 Daniel Roe <daniel.r.roe.gmail.com>:
> 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed May 21 2014 - 01:00:02 PDT
