[AMBER] about rms atomic fluctuation for protein crystal .thank you very much!

From: Yongxiu Li <lyx.itcs.ecnu.edu.cn>
Date: Mon, 14 Oct 2013 19:36:06 +0800

Dear everyone,
      I want to construct the unit cell as the tutorial13 and do the
same work as the David A. Case's paper "Simulations of a protein crystal
with a high resolution X-ray structure: Evaluation of force fields and
water models." /J. Phys. Chem. B/ *114*:12811-12824. Different from the
paper, we construct the simulation Cell from 108 individual unit cells
in a 3*3*3 arrangement and simulate the system for 150ns using amber
FF99SB force field and TIP3P water.
     After simulation, I use the 'BasicAnalysis.sh' script in
AmberTools/src/xtalutil/Analysis to do each step analysis. Each step is
the same as BasicAnalysis.sh but all atomic positions haven't rescaled
at any steps. After many steps' analysis, we use the
'analyse_revsym.py' to analyse the last 100ns bfactor . I understand
that figure8 is the bfac_lat_calpha.dat in this script and figure9 is
the bfac_asu_calpha.dat . I want to know whether I misunderstand to
distinguish this two figure and their analysis script . Compared with
figure8 in Case's paper,why the bfac_lat_calpha.dat which I gained is so
big.

the scipt is that :
Because the paper said in figure9 the atomic fluctuations were computed
on the basis of the distribution of each atom obtained after optimal
quaternion alignments of the protein backbones. I do a little
modification in ctraj_bfactor_asu(rms reference mass :1-64&!(.H=)
changed to rms reference mass :1-64.CA,C,N).
Best wishes!
Aimee Li

In the attachmet, amber-3-3-3.png is the bfactor. and figure 8 and
figure9 are the pictures in Case's paper.
next two script are using to compute the bfactor.
ctraj_bfactor_asu:
parm asu.prmtop
trajin RevSym_01_01.nc 25001 75000
trajin RevSym_01_02.nc 25001 75000
......
trajin RevSym_27_03.nc 25001 75000
trajin RevSym 27_04.nc 25001 75000
reference AvgCoord_asu.rst7.1
rms reference mass :1-64.CA,C,N
atomicfluct out bfac_asu_calpha :1-64.CA byatom bfactor
atomicfluct out bfac_asu_sdch :1-64&!(.H=,CA,C,O,N) byres bfactor
atomicfluct out bfac_asu_bkbn :1-64.CA,C,N byres bfactor
atomicfluct out bfac_asu_all :1-64 byres bfactor

and ctraj_bfactor_lat:
parm asu.prmtop
trajin RevSym_01_01.nc 25001 75000
trajin RevSym_01_02.nc 25001 75000
......
trajin RevSym_27_03.nc 25001 75000
trajin RevSym 27_04.nc 25001 75000
atomicfluct out bfac_lat_calpha.dat :1-64.CA byatom bfactor
atomicfluct out bfac_lat_sdch.dat :1-64&!(.H=,CA,C,O,N) byres bfactor
atomicfluct out bfac_lat_bkbn.dat :1-64.CA,C,N byres bfactor
atomicfluct out bfac_lat_all.dat :1-64 byres bfactor


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figure9.png
(image/png attachment: figure9.png)

figure8.png
(image/png attachment: figure8.png)

amber-3-3-3.png
(image/png attachment: amber-3-3-3.png)

Received on Mon Oct 14 2013 - 05:00:02 PDT
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