AMBER Archive (2002)

Subject: RE: atomicfluct in ptraj

From: Kristina Furse (kristina.e.furse_at_vanderbilt.edu)
Date: Thu Dec 19 2002 - 13:28:16 CST

I didn't alter the coordinates at all before performing the atomicfluct
calculation--should the coordintes be centered or rms fitted to the first
frame before calculating the atomic fluctuations or is this taken care of
within the atomicfluct command? So basically, is the drift I'm seeing a
translational/rotational drift, or a conformational one?

Sorry about the lack of numerical information--there are 1106 residues (COX
dimer again), so it's a little much in tabular form. I've included a few
exerpts below. The biggest difference is for res 554 (131 for 300ps vs 17-67
for the 50ps sections), which is the N-terminus of the second chain.

Thanks,

Kristina

Frame ***300ps*** **50ps(3rd)** **50ps(6th)**
      1 34.892101 13.214636 25.813904
      2 17.341350 9.510433 11.533652
      3 11.668477 5.901847 7.025210
      4 9.323540 6.413303 6.135395
      5 8.187171 5.644763 4.316591
      6 9.064189 5.168338 4.150105
      7 11.077648 6.464721 4.314197
      8 14.017268 6.900782 4.663157
      9 13.443498 3.930454 5.484204
     10 10.562475 3.465813 3.912770
     11 15.713521 4.817442 3.247160
     12 16.532082 6.889063 3.360368
     13 10.613699 5.193647 4.243640
     14 7.810770 4.976791 5.317102
     15 6.121783 3.569330 3.457971
     16 5.559723 3.639051 3.319167
     17 7.392832 4.820106 3.755249
     18 9.700404 6.335829 5.862608
     19 19.397092 8.541331 6.510045
     20 28.085005 10.090056 10.102773
     21 32.518542 19.761230 17.377652
     22 26.837089 24.987433 15.544742
     23 16.856022 11.247345 11.880345
     24 8.755815 6.895355 6.500217
     25 8.539308 5.581510 4.372993

    231 8.773181 3.948159 4.692612
    232 8.321950 3.896068 5.048935
    233 14.848439 6.453182 6.474735
    234 18.433247 5.805861 6.900778
    235 18.608312 6.983041 6.938564
    236 41.572617 10.377426 10.454082
    237 44.494473 15.425113 14.921916
    238 28.491382 12.300204 8.660919
    239 26.170560 9.526663 8.862232
    240 15.150656 8.049962 6.846571
    241 12.514764 9.037012 7.995837

    550 6.965376 3.908251 3.157328
    551 6.803795 3.626815 3.577019
    552 11.208570 8.282142 4.819026
    553 23.710455 12.565157 9.362678
    554 131.762136 17.575238 67.535223
    555 53.503953 14.344769 17.629723
    556 28.886783 6.916022 11.631196
    557 15.685219 6.072493 8.427692
    558 10.397657 5.281013 5.395450
    559 11.033106 6.505656 4.668846
    560 11.575775 6.868934 6.587854

>===== Original Message From amber_at_heimdal.compchem.ucsf.edu =====
>On Wed, Dec 18, 2002, Kristina Furse wrote:
>>
>> Had a question about the calculation of atomic fluctuation in ptraj. I
>> wanted to compare the Bfactors for the CA's of my protein in 50ps subsets
of
>> a 300ps trajectory to each other and to Bfactors calculated for the whole
>> traj, as one indication that the system is equilibrating. When I did this,
>> the resulting Bfactors for the enitire 300ps run were larger than the
>> average of the 6 subsets. Does this sound right? Can the whole thing be
more
>> than the avererage of its parts? Would this possibly reflect some kind of
>> net movement?
>
>This is indeed to be expected, and reflects both the fact that it takes a
>finite time for fluctuations to "build up", and (in most cases) the fact that
>there can be a slow overall "drift" in the mean structure. Especially for so
>short a simulation, what you report is not unexpected. (Without knowing the
>actual numbers, or how much bigger they are for 300 ps than for 50 ps, I
can't
>say much more.)
>
>.good luck...dac
>
>--
>
>==================================================================
>David A. Case | e-mail: case_at_scripps.edu
>Dept. of Molecular Biology, TPC15 | fax: +1-858-784-8896
>The Scripps Research Institute | phone: +1-858-784-9768
>10550 N. Torrey Pines Rd. | home page:
>La Jolla CA 92037 USA | http://www.scripps.edu/case
>==================================================================

****************************************************
Kristina E. Furse
Department of Chemistry
Center for Structural Biology
Vanderbilt University
email: kfurse_at_structbio.vanderbilt.edu