Respected sir,
Yeah I did that. This is complete protocol. I have attached the file atomicfluct data document in case the things get messy in email.
trajin combined50ns.mdcrd
autoimage
reference combined50ns_average_protein.pdb [avgxray]
rms !:WAT,Na+,Cl-,UNK ref [avgxray]
atomicfluct out combined50ns_atomicfluct.dat '!.H,N,CA,HA,C,O &!:WAT,Na+,Cl-'byres bfactor
atomicfluct out combined50ns_atomicfluct_byatom.dat '!.H,N,CA,HA,C,O &!:WAT,Na+,Cl-'byatom bfactor
for atomic fluctuations it is advisable to consider whole protein or only side chains?
one more query regarding RMSD. Though I understood that for complete protein or small peptide 2 Ang value can't be considered a criteria BUT is the same valid for small molecules or while comparing single amino acid in a protein.
Thanks and regards,
Nitin Sharma
-----Original Message-----
From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
Sent: Monday, January 06, 2014 2:28 AM
To: AMBER Mailing List
Subject: Re: [AMBER] standard for atomic fluctioantion
Hi,
Did you remove global rotational translational motion from your system prior to 'atomicfluct'? If you do not, contributions from these motions will be present in the calculated fluctuations. As mentioned in the manual:
"If you want fluctuations without rotations or translations (for example to the average structure), perform an RMS fit to the average structure (best) or the first structure (see rmsd ) prior to this calculation."
-Dan
On Sun, Jan 5, 2014 at 5:47 AM, Nitin Sharma <sharmanitin.nus.edu.sg> wrote:
> Respected sir,
>
>
>
> Thanks for the reply. I can observe from my results that value of RMSD
> shows following trend backbone < complete residues < side chain. I
> think this is due to the fact that side chain are more flexible than backbone.
> Hence, your statement that same 2 Ang should not be used in all three
> cases makes sense and so do in the case of large and small systems
> where combined effect of all systems can effect RMSD values.
>
>
>
> Taking your advice I did measure atomic fluctuation by using bfactor
> according to following command
>
>
>
> atomicfluct out combined_atomicfluct.dat '!.H,N,CA,HA,C,O &!:WAT,Na+,Cl-'
> byres bfactor
>
>
>
> however, I was not able to analyse the results. Thus I calculated it
> again but this time using byatom instead of byres and hoping to find
> any relation between the bfactor present in pdb file using following
> command
>
>
>
> atomicfluct out combined_atomicfluct_byatom.dat '!.H,N,CA,HA,C,O
> &!:WAT,Na+,Cl-' byatom bfactor
>
>
>
> I was still not able to find anything conclusive and for me it was
> just a set of number. I excluded backbone from the calculation for
> atomic fluctuation. Is this a valid approach or I should have taken
> whole residue into account ?
>
>
>
>
> #Atom
>
> atomicfluct_byatom
>
> #Res
>
> atomicfluct_byres
>
> ATOM 1 N GLY A 171 6.051 3.937 10.438 1.00 42.81
> N1+
>
> 2
>
> 142.6051
>
> 1
>
> 114.1471
>
> ATOM 2 CA GLY A 171 4.779 4.108 9.759 1.00 32.15
> C
>
> 3
>
> 143.4394
>
> 2
>
> 28.7242
>
> ATOM 3 C GLY A 171 3.640 3.323 10.383 1.00 19.83
> C
>
> 4
>
> 142.8212
>
> 3
>
> 37.9309
>
> ATOM 4 O GLY A 171 3.824 2.531 11.310 1.00 27.74
> O
>
> 6
>
> 69.2032
>
> 4
>
> 29.1104
>
> ATOM 5 HA2 GLY A 171 4.539 5.048 9.767 1.00 38.58
> H
>
> 7
>
> 72.6666
>
> 5
>
> 37.6553
>
> ATOM 6 HA3 GLY A 171 4.871 3.826 8.835 1.00 38.58
> H
>
> 14
>
> 14.1067
>
> 6
>
> 22.1069
>
> ATOM 7 N ASP A 172 2.445 3.561 9.850 1.00 15.99
> N
>
> 15
>
> 19.7028
>
> 7
>
> 35.5631
>
> ATOM 8 CA ASP A 172 1.216 2.928 10.304 1.00 15.83
> C
>
> 16
>
> 17.6406
>
> 8
>
> 6.8956
>
> ATOM 9 C ASP A 172 1.093 1.510 9.699 1.00 12.28
> C
>
> 17
>
> 12.7972
>
> 9
>
> 20.1038
>
> ATOM 10 O ASP A 172 0.821 1.376 8.501 1.00 13.61
> O
>
> 18
>
> 52.2442
>
> 10
>
> 37.7367
>
> ATOM 11 CB ASP A 172 0.065 3.834 9.836 1.00 17.97
> C
>
> 19
>
> 29.3983
>
> 11
>
> 16.4365
>
> ATOM 12 CG ASP A 172 -1.296 3.351 10.265 1.00 22.19
> C
>
> 26
>
> 16.7257
>
>
>
> ATOM 13 OD1 ASP A 172 -1.395 2.210 10.733 1.00 19.08
> O
>
> 27
>
> 20.907
>
>
>
> ATOM 14 OD2 ASP A 172 -2.281 4.118 10.119 1.00 26.85
> O1-
>
> 28
>
> 19.1486
>
>
>
> ATOM 15 H ASP A 172 2.319 4.109 9.199 1.00 19.19
> H
>
> 29
>
> 21.1538
>
>
>
> ATOM 16 HA ASP A 172 1.205 2.866 11.282 1.00 19.00
> H
>
> 30
>
> 28.0041
>
>
>
> ATOM 17 HB2 ASP A 172 0.196 4.721 10.206 1.00 21.57
> H
>
> 31
>
> 22.5693
>
>
>
> ATOM 18 HB3 ASP A 172 0.074 3.876 8.867 1.00 21.57
> H
>
> 32
>
> 25.1447
>
>
>
> ATOM 19 N GLU A 173 1.322 0.462 10.499 1.00 13.30
> N
>
> 33
>
> 64.2233
>
>
>
> ATOM 20 CA GLU A 173 1.308 -0.904 9.951 1.00 13.59
> C
>
>
>
>
>
>
>
> ATOM 21 C GLU A 173 -0.094 -1.333 9.497 1.00 13.08
> C
>
>
>
>
>
>
>
> ATOM 22 O GLU A 173 -0.236 -2.099 8.524 1.00 13.46
> O
>
>
>
>
>
>
>
> ATOM 23 CB GLU A 173 1.863 -1.920 10.953 1.00 18.28
> C
>
>
>
>
>
>
>
> ATOM 24 CG GLU A 173 1.623 -3.401 10.580 1.00 24.97
> C
>
>
>
>
>
>
>
> ATOM 25 CD GLU A 173 2.448 -3.911 9.387 1.00 49.28
> C
>
>
>
>
>
>
>
> ATOM 26 OE1 GLU A 173 3.366 -3.192 8.927 1.00 27.07
> O
>
>
>
>
>
>
>
> ATOM 27 OE2 GLU A 173 2.176 -5.047 8.908 1.00 30.55
> O1-
>
>
>
>
>
>
>
> ATOM 28 H GLU A 173 1.485 0.510 11.343 1.00 15.96
> H
>
>
>
>
>
>
>
> ATOM 29 HA GLU A 173 1.889 -0.924 9.162 1.00 16.31
> H
>
>
>
>
>
>
>
> ATOM 30 HB2 GLU A 173 2.821 -1.788 11.028 1.00 21.94
> H
>
>
>
>
>
>
>
> ATOM 31 HB3 GLU A 173 1.445 -1.763 11.815 1.00 21.94
> H
>
>
>
>
>
>
>
> ATOM 32 HG2 GLU A 173 1.844 -3.953 11.346 1.00 29.96
> H
>
>
>
>
>
>
>
> ATOM 33 HG3 GLU A 173 0.685 -3.515 10.357 1.00 29.96
> H
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> Can you please help me in analyzing the atomic fluctuation result.
>
>
>
> Thanks in advance.
>
>
>
> Nitin Sharma
>
>
>
> -----Original Message-----
> From: Daniel Roe [mailto:daniel.r.roe.gmail.com]
> Sent: Sunday, January 05, 2014 2:35 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] standard for atomic fluctioantion
>
>
>
> Hi,
>
>
>
> On Sat, Jan 4, 2014 at 10:09 AM, Nitin Sharma <sharmanitin.nus.edu.sg
> <mailto:sharmanitin.nus.edu.sg>>wrote:
>
>
>
> > I am aware of the 2 Angstrom as a benchmark for RMSD but is there
> > any
>
> > benchmark for atomic fluctuation too? How I can say by looking just
> > at
>
> > atomic fluctuation result which residue is moving within acceptable
>
> > range and which is not?
>
> >
>
>
>
> I'm actually wary of calling 2 Angstroms a "benchmark" for RMSD, by
> which I assume you mean something like a cut-off for determining a 'native' state.
>
> This number is going to be both system dependent (e.g. 2 Ang. for a 5
> residue polypeptide may be too large a cut-off, while 2 Ang. for a
> 700+ residue peptide may be too small) and selection dependent (i.e.
> all-atom versus backbone atoms versus mass-weighted, etc). You will
> need to look at the actual behavior of your system to determine what a
> reasonable cut-off is. If you're trying to do something like determine
> a melting curve, your results could be quite sensitive to how you choose your cut-off.
>
>
>
> Similarly, I don't believe there is one value that atomic fluctuations
> should be compared to - they will be system dependent as well. For
> atomic fluctuations you ideally want to compare to some experimental
> measure of atomic mobility such as B-factors from an X-ray crystal
> structure (for which you can use the 'bfactor' keyword with the
> 'atomicfluct' command in cpptraj / ptraj).
>
>
>
> Hope this helps,
>
>
>
> -Dan
>
>
>
> --
>
> -------------------------
>
> 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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>
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>
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
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>
--
-------------------------
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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- application/vnd.openxmlformats-officedocument.wordprocessingml.document attachment: Atomicfluct_data.docx
Received on Sun Jan 05 2014 - 11:00:02 PST
