Thanks Daniel, yes I meant 'AMBER' as cpptraj. I think I should get rid of
Hs and match heavy atoms.
On Wed, Sep 17, 2014 at 6:02 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> On Wed, Sep 17, 2014 at 8:56 AM, newamber list <newamberlist.gmail.com>
> wrote:
> >>> No, as long as the number of atoms and the atom ordering in your target
> > and reference structures are the same.
> >
> > I thought the RMS fitting can take care. Actually AMBER does not complain
> > about atom names and ordering/sequence. So do I need to keep same atom
> > names and ordering?
>
> (By AMBER do you specifically mean cpptraj?)
>
> In order for your RMSD calculation to be meaningful the atoms selected
> in your target should correspond to the atoms selected in your
> reference. Take the two sequences you posted for example. If you were
> to specify something like:
>
> rms reference .1-5 out rmsd.dat
>
> this calculation will proceed because the same number of atoms are
> selected in both the target and the reference. However, the ordering
> does *not* match. If the first sequence is your target and the second
> is your reference, these are how the atoms line up:
>
> O5' | HO5'
> H5T | O5'
> C5' | C5'
> 1H5' | H5'
> 2H5' | H5''
>
> The first two atom pairs being compared are clearly mismatches, which
> will serve to artificially inflate the resulting RMSD. However, it may
> be the case that the heavy atom ordering is the same between both
> structures. If that is true (as it often is for e.g. amino acid
> backbone atoms, N, CA, C) you can use the atom mask to ensure atoms
> line up, e.g.:
>
> rms reference !.H= out rmsd.dat
>
> O5' | O5'
> C5' | C5'
> etc.
>
> It's up to you to ensure you are making a "good" atom selection.
> Typically you will be able to tell a "bad" selection because the RMSD
> values will be unusually high, but this is not always the case. The
> 'select' or 'atoms' commands in cpptraj can be useful for testing out
> atom selections.
>
> Hope this helps,
>
> -Dan
>
> >
> > e.g. comparing say first few atoms in structure to be compared (in
> > trajectory) has this sequence
> >
> > ATOM 1 O5' DG 1 88.750 97.070 107.880 1.00
> > 0.00
> > ATOM 2 H5T DG 1 89.730 97.100 108.050 1.00
> > 0.00
> > ATOM 3 C5' DG 1 88.150 98.370 108.180 1.00 0.00
> > ATOM 4 1H5' DG 1 88.610 99.040 107.590 1.00
> > 0.00
> > ATOM 5 2H5' DG 1 88.360 98.560 109.130 1.00 0.00
> >
> >
> > and the reference structure has this:
> >
> > ATOM 1 HO5' DG5 1 12.843 -51.888 -5.899 1.00
> > 0.00 H
> > ATOM 2 O5' DG5 1 13.094 -52.038 -5.621 1.00
> > 0.00 O
> > ATOM 3 C5' DG5 1 13.037 -51.978 -4.813 1.00
> > 0.00 C
> > ATOM 4 H5' DG5 1 13.096 -51.378 -4.805 1.00
> > 0.00 H
> > ATOM 5 H5'' DG5 1 13.617 -52.139 -4.669 1.00
> > 0.00 H
> >
> > Thanks
> >
> >
> > On Mon, Sep 8, 2014 at 2:54 PM, Daniel Roe <daniel.r.roe.gmail.com>
> wrote:
> >
> >> Hi,
> >>
> >> On Sun, Sep 7, 2014 at 8:52 PM, Yip Yew Mun <yipy0005.gmail.com> wrote:
> >> > Hi, I recently ran a simulation of a small alpha helix (~12 residues)
> >> with REMD and I did a RMSD analysis using just the backbone atoms
> (N,CA,C).
> >> Usually for simulations of large proteins, an RMSD of 3 Angstroms is
> >> usually enough to quantify that there are no major conformational
> changes.
> >> However, I realised for small protein systems like mine, an RMSD of 3
> >> Angstroms isn’t a good criterion to say that I have folded my protein
> >> successfully. Therefore, I wish to ask:
> >> >
> >> > 1) Does the number of atoms affect the RMSD calculation?
> >>
> >> For folded conformations not really. Average RMSD is not correlated
> >> with chain length, although the distribution tends to get narrower for
> >> longer chains.
> >>
> >> > 2) Is there a need for the reference structure to be protonated before
> >> using it for RMSD analysis since in this case, I’m just using the
> backbone
> >> atoms (N,CA,C).
> >>
> >> No, as long as the number of atoms and the atom ordering in your
> >> target and reference structures are the same. Jed Pitera has recently
> >> done some very interesting work looking at intrinsic characteristics
> >> of RMSD distributions that I recommend checking out:
> >> http://pubs.acs.org/doi/abs/10.1021/jp412776d
> >>
> >> Hope this helps,
> >>
> >> -Dan
> >>
> >> >
> >> > Thanks.
> >> >
> >> > Yip Yew Mun (Mr) | PhD Research Scholar | Division of Chemistry &
> >> Biological Chemistry
> >> > School of Physical & Mathematical Sciences | Nanyang Technological
> >> University | Singapore 639798
> >> > Tel: (+65) 97967803 | Email: yipy0010.e.ntu.edu.sg | GMT+8h
> >> >
> >> > _______________________________________________
> >> > 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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> > 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 Wed Sep 17 2014 - 10:30:03 PDT
