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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>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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--
-------------------------
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 - 10:30:02 PDT
