I want to do principal analysis of 1ns MD simulation (center of mass
translational motion has been removed during the MD simulation at periodic
time intervals) of a protein in order to calculate fluctuation on CA atoms
in the lowest frequency mode. I found that for the same simulation data,
having "rms first *" command in the analysis script or not having "rms
first *" command
will render different results. That is, if I use the pca analysis script as
the following:
------------------------------------------------------------------------------------------------------------------------
/soft/linux/pkg/amber8_070104/exe.serial/ptraj ../parm/monP.prmtop
<<script
trajin ../output/mw.1.nptL.mdcrd
reference ../parm/monP.prmcrd
strip :WAT
strip :Cl-
image
rms first *
matrix mwcovar .CA name mwcovarmat out mwcovarmat.dat
analyze matrix mwcovarmat out wt_mwevec.pev name mwevecs vecs 15
analyze modes fluct out wtrmsfluc_1 stack mwevecs beg 1 end 1
go
script
end
------------------------------------------------------------------------------------------------------------------------
the output wtrmsfluct_1 is :
------------------------------------------------------------------------------------------------------------------------
Analysis of modes: RMS FLUCTUATIONS
Atom no. rmsX rmsY rmsZ rms
1 0.143 0.057 0.160 0.222
2 0.151 0.070 0.183 0.248
3 0.151 0.055 0.126 0.204
4 0.150 0.055 0.091 0.184
5 0.151 0.053 0.048 0.167
6 0.167 0.061 0.024 0.179
7 0.182 0.069 0.020 0.196
8 0.187 0.014 0.094 0.210
9 0.092 0.019 0.090 0.130
10 0.092 0.060 0.089 0.141
11 0.129 0.063 0.000 0.144
12 0.735 0.082 0.895 1.161
13 0.903 0.055 1.235 1.531
14 1.009 0.612 0.317 1.222
15 0.396 0.061 0.063 0.405
16 0.274 0.305 0.195 0.454
17 0.374 0.276 0.580 0.743
18 0.261 0.021 0.177 0.316
..... ......... ......... ......... ..........
--------------------------------------------------------------------------------------------------------------------------
But if I delete "rms first *" and rerun the pca analysis, the output
wtrmsfluct_1 will be:
-------------------------------------------------------------------------------------------------------------------------------
Analysis of modes: RMS FLUCTUATIONS
Atom no. rmsX rmsY rmsZ rms
1 0.014 0.006 0.012 0.019
2 0.002 0.006 0.008 0.010
3 0.005 0.002 0.010 0.011
4 0.005 0.004 0.004 0.008
5 0.007 0.001 0.015 0.017
6 0.021 0.001 0.005 0.021
7 0.039 0.011 0.003 0.041
8 0.011 0.042 0.006 0.044
9 0.068 0.072 0.014 0.101
10 0.056 0.128 0.113 0.179
11 0.288 0.139 0.135 0.347
12 0.932 0.046 0.977 1.351
13 1.145 0.077 1.355 1.775
14 1.225 0.719 0.529 1.516
15 0.701 0.248 0.180 0.765
16 0.451 0.124 0.021 0.469
17 0.242 0.433 0.415 0.646
18 0.172 0.067 0.063 0.194
..... ......... ......... ......... ..........
-------------------------------------------------------------------------------------------------------------------------------
Would someone please tell me that if the rms fitting is actually needed
here in the pca analysis?
Any help or suggestion on this is greatly appreciated.
sincerely
jianping
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Received on Wed Jan 18 2006 - 06:10:08 PST
