Hi,
The key message here from cpptraj is, "This is expected for Proline
and terminal/non-standard residues". If you look closely at the MET
residue you pasted (which is clearly N-terminal MET), you have H1, H2,
and H3 bonded to N, but not 'H' (i.e. backbone amide hydrogen), which
is the name that the 'secstruct' command is looking for. Assuming that
all of the MET residues you listed are terminal residues you can
safely ignore the warning. Hope this helps,
-Dan
On Mon, Sep 21, 2015 at 8:16 AM, Fabian gmail <fabian.glaser.gmail.com> wrote:
> Dear amber colleagues,
>
> I am running simulations with several peptides on a box 6 in total, which goes very well, amber runs perfectly, I get the trajectories, etc. But when I use cpptraj to read the trajectory, which also goes well and I can do everything, I get the following warning
>
> Warning: Not all BB atoms found for 6 residues: MET:1 MET:23 MET:45 MET:67 MET:89 MET:111
> Info: This is expected for Proline and terminal/non-standard residues.
> Info: Expected BB atom names: N=[N ] H=[H ] C=[C ] O=[O ] CA=[CA ]
>
> But when I prepare the input with tleap (after chimera editing), there is no warning when I save the .prmtop or the .pdb file, here is the beginning of one of the peptides, it looks that it have all the atoms mentioned on the warning to me...
>
>
> ATOM 1 N MET 1 -3.466 15.214 -25.205 1.00 0.00
> ATOM 2 H1 MET 1 -3.034 16.124 -25.268 1.00 0.00
> ATOM 3 H2 MET 1 -4.470 15.318 -25.182 1.00 0.00
> ATOM 4 H3 MET 1 -3.204 14.660 -26.008 1.00 0.00
> ATOM 5 CA MET 1 -3.015 14.539 -23.976 1.00 0.00
> ATOM 6 HA MET 1 -3.213 15.152 -23.097 1.00 0.00
> ATOM 7 CB MET 1 -3.628 13.184 -23.837 1.00 0.00
> ATOM 8 HB2 MET 1 -2.845 12.432 -23.935 1.00 0.00
> ATOM 9 HB3 MET 1 -4.360 13.042 -24.633 1.00 0.00
> ATOM 10 CG MET 1 -4.298 13.007 -22.527 1.00 0.00
> ATOM 11 HG2 MET 1 -4.968 13.843 -22.329 1.00 0.00
> ATOM 12 HG3 MET 1 -3.554 12.928 -21.735 1.00 0.00
> ATOM 13 SD MET 1 -5.235 11.464 -22.657 1.00 0.00
> ATOM 14 CE MET 1 -6.530 12.162 -23.658 1.00 0.00
> ATOM 15 HE1 MET 1 -7.266 11.393 -23.889 1.00 0.00
> ATOM 16 HE2 MET 1 -6.104 12.547 -24.586 1.00 0.00
> ATOM 17 HE3 MET 1 -7.011 12.975 -23.115 1.00 0.00
> ATOM 18 C MET 1 -1.557 14.264 -24.121 1.00 0.00
> ATOM 19 O MET 1 -1.099 13.845 -25.166 1.00 0.00
>
> why do I get this warning if all the mentioned atoms are there…. for every peptide???
>
> Should I do something about it?
>
> Again everything goes well on tleap when preparing the box etc.
>
> Thanks a lot in advance,
>
> Fabian
>
> ____________________
> Dr. Fabian Glaser
> Head of the Structural Bioinformatics section
> Bioinformatics Knowledge Unit - BKU
>
> fglaser.technion.ac.il
> Tel: +972 4 8293701
>
> http://bku.technion.ac.il
> The Lorry I. Lokey Interdisciplinary
> Center for Life Sciences and Engineering
> Technion - Israel Institute of Technology
> Haifa 32000, ISRAEL
>
>
> _______________________________________________
> AMBER mailing list
> 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 307
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 Mon Sep 21 2015 - 08:00:03 PDT
