Thanks!
Yes all of them are nterm great!
Fabian
On Sep 21, 2015 5:55 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> 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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>
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Received on Mon Sep 21 2015 - 09:30:04 PDT
