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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Received on Sun Jan 05 2014 - 05:00:02 PST
