Dear Amber
I followed the tutorial for PCA (
http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/) , Probably I am
not understanding it properly , if little explanation is given in the usage
it will be more helpful for me
I have given my input and error files as below.
thank you
I prepared the input file as below
---------------------
parm complex.prmtop
trajin md1.mdcrd parm
rms first :1-340&!.H=
average crdset cpu-average.pdb pdb
createcrd md2_cpu_average
run
crdaction md2_cpu_average rms reference cpu-average.pdb :1-340&!.H=
crdaction md2_cpu_averag matrix covar \
name cpu-covar :1-340&!.H=
analysis diagmatrix cpu-covar out cpu-evecs.dat \
vecs 3 name myEvecs \
nmwiz nmwizvecs 3 nmwfile out.nmd nmwizmask :1-340&!.H=
crdaction trajectories projection CPU modes myEvecs \
beg 1 end 3 :1-36&!.H= crdframes 0,20000
hist CPU:1 bins 100 out cpu-gpu-hist.agr norm name CPU-1
hist CPU:2 bins 100 out cpu-gpu-hist.agr norm name CPU-2
hist CPU:3 bins 100 out cpu-gpu-hist.agr norm name CPU-3
run
clear all
readdata cpu-evecs.dat name Evecs
parm complex.prmtop
parmstrip !(:1-36&!.H=)
parmwrite out cpu-modes.prmtop
runanalysis modes name Evecs trajout cpu-gpu-mode1.nc \
pcmin -100 pcmax 100 tmode 1 trajoutmask :1-36&!.H= trajoutfmt netcdf
---------------------
-------------------------
*I got the error message *
DATASETS:
2 data sets:
RMSD_00000 "RMSD_00000" (double, rms), size is 20000
md2_cpu_average "md2_cpu_average" (coordinates), size is 20000 (1273 MB)
5562 atoms
---------- RUN END ---------------------------------------------------
[crdaction md2_cpu_average rms reference cpu-average.pdb :1-340&!.H=]
Error: No reference frames defined.
1 errors encountered reading input.
TIME: Total execution time: 120.7571 seconds.
-----------------------------
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Received on Thu Jun 09 2016 - 11:30:02 PDT
