Dear Amber Users,
I am trying to perform principal component
analysis in cpptraj. The input script is the following:
*parm 6ted_EC_dry.psftrajin combined_stride10.dcd 25001 last 5rms first
:1-7919&!.H=average crdset 6ted_pcacreatecrd 6ted_trajectoryruncrdaction
6ted_trajectory rms ref 6ted_pca .N,CA,Ccrdaction 6ted_trajectory matrix
covar name 6ted_pca_covar .N,CA,Crunanalysis diagmatrix 6ted_pca_covar out
6ted_eig_vec.dat vecs 5 name myEvecs nmwiz nmwizvecs 5 nmwizfile
6ted_pca1.nmd nmwizmask .N,CA,Crunclear allreaddata 6ted_eig_vec.dat name
Evecsparm 6ted_EC_dry.psfparmstrip !(:1-7919.N,CA,C)parmwrite out
6ted_modes.prmtoprunanalysis modes name Evecs trajout 6ted_mod1.nc
<
http://6ted_mod1.nc> pcmin -100 pcmax 100 tmode 1 trajoutmask .N,CA,C
trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod2.nc
<
http://6ted_mod2.nc> pcmin -100 pcmax 100 tmode 2 trajoutmask .N,CA,C
trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod3.nc
<
http://6ted_mod3.nc> pcmin -100 pcmax 100 tmode 3 trajoutmask .N,CA,C
trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod4.nc
<
http://6ted_mod4.nc> pcmin -100 pcmax 100 tmode 4 trajoutmask .N,CA,C
trajoutfmt netcdfrunanalysis modes name Evecs trajout 6ted_mod5.nc
<
http://6ted_mod5.nc> pcmin -100 pcmax 100 tmode 5 trajoutmask .N,CA,C
trajoutfmt netcdf*
*But while running the script, I am getting the following error:*
*Warning: No atoms in mask ':1-7919&.CA,N,C'*
My system is relatively large. I tried running PCA without hydrogen, but it
failed due to memory issues.(terminate called after throwing an instance of
'std::bad_alloc'
what(): std::bad_alloc
/var/spool/slurm/job1675329/slurm_script: line 9: 2989244 Aborted
(core dumped))
Hence, I tried it with the backbone. I do not know what is wrong with the
musk. Any help will be greatly appreciated.
Regards
Tanmoy
--
With regards,
Tanmoy
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Received on Sat Jun 03 2023 - 23:00:02 PDT
