I would appreciate some guidance regarding this. Thanks in advance.
On Mon, Dec 12, 2022 at 10:51 AM Prithviraj Nandigrami <
prithviraj.nandigrami.gmail.com> wrote:
> Dear AMBER Experts,
>
> I am trying to perform PCA using cpptraj using the following script
> (combining multiple trajectories from independent MD runs):
>
> # RMS-Fit to first frame to remove global translation/rotation
> parm REF/OPEN_WT/run1/step5_input.parm7
> trajin REF/OPEN_WT/run1/combined_longrun.nc
> trajin REF/OPEN_WT/run2/combined_longrun.nc
> trajin REF/OPEN_WT/run3/combined_longrun.nc
> center
> autoimage
> rms ToFirst :1-438&!.H=
> average crdset avg_set
> createcrd traj_set
> run
>
> crdaction traj_set rms ref avg_set
> :4-34,51-90,121-150,155-183,241-271,280-306,333-360,366-394.CA&!.H=
>
> crdaction traj_set matrix covar \
> :4-34,51-90,121-150,155-183,241-271,280-306,333-360,366-394.CA&!.H= name
> WT_covar \
> out output_combined.PCA_backbone/OPEN_WT/WT_covmat.dat #Write covariance
> matrix based on given selection mask
>
>
>
> *runanalysis diagmatrix WT_covar out
> output_combined.PCA_backbone/OPEN_WT/WT_evecs.dat \ vecs 5 name myevecs
> nmwiz nmwizvecs 5 nmwizfile
> output_combined.PCA_backbone/OPEN_WT/WT_porcupine.nmd \ nmwizmask
> :4-34,51-90,121-150,155-183,241-271,280-306,333-360,366-394.CA&!.H=*
>
> crdaction traj_set projection p1 modes myevecs beg 1 end 5
> :4-34,51-90,121-150,155-183,241-271,280-306,333-360,366-394.CA&!.H= \
> out output_combined.PCA_backbone/OPEN_WT/WT_open_pca-5.dat #write
> projections of first 5 PCs
>
> hist p1:1 bins 100 out output_combined.PCA_backbone/OPEN_WT/WT-hist.agr
> norm name WT-1
> hist p1:2 bins 100 out output_combined.PCA_backbone/OPEN_WT/WT-hist.agr
> norm name WT-2
> hist p1:3 bins 100 out output_combined.PCA_backbone/OPEN_WT/WT-hist.agr
> norm name WT-3
> hist p1:4 bins 100 out output_combined.PCA_backbone/OPEN_WT/WT-hist.agr
> norm name WT-4
> hist p1:5 bins 100 out output_combined.PCA_backbone/OPEN_WT/WT-hist.agr
> norm name WT-5
>
> run
>
> clear all
>
> readdata output_combined.PCA_backbone/OPEN_WT/WT_evecs.dat name Evecs
>
> parm REF/OPEN_WT/run1/step5_input.parm7
> parmstrip !(:4-34,51-90,121-150,155-183,241-271,280-306,333-360,366-394.CA
> &!.H=)
> parmwrite out output_combined.PCA_backbone/OPEN_WT/modes.prmtop
>
> runanalysis modes name Evecs trajout
> output_combined.PCA_backbone/OPEN_WT/WT-mode1.nc \
> pcmin -100 pcmax 100 tmode 1 trajoutmask
> ::4-34,51-90,121-150,155-183,241-271,280-306,333-360,366-394.CA&!.H=
> trajoutfmt netcdf
>
>
>
> I am running this script for different systems (wild-type protein, mutant
> etc.). Instead of the default "porcupine" visualization showing the
> direction and variance of different PCs, I was interested in calculating a
> "difference" vector between the single mutant and WT by changing the bold
> highlighted lines above where I print out a difference in vectors between
> the mutant and WT systems from within the script directly. Is there a way
> to do this inside the script or do I have to post-process it after writing
> out the vectors for the WT and mutant systems?
>
> Any help/guidance would be greatly appreciated.
>
> Best regards,
> P.N.
>
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Received on Thu Dec 15 2022 - 15:00:03 PST
