From: Elvis Martis <>
Date: Fri, 10 Feb 2017 01:26:36 +0000


Have you edited the script to add correct file names that you are interested in??

I see at some places you have now updated the atom mask.

                   Best Regards


Elvis Martis
Ph.D. Student (Computational Chemistry)
 at Bombay College of Pharmacy

A Kalina, Santacruz [E], Mumbai 400098, INDIA
Skype. adrian_elvis12<>


From: Thakur, Abhishek <>
Sent: 10 February 2017 03:50:48
Subject: [AMBER] PCA

Hi I am very new to PCA analysis.

I am getting an error

Error: # selected coords (8238) != eigenvector size (855)

/: Permission denied.

While using following script, can anyone help e out in solving it?

trajin /projects/chem/ionic/abhi/PRMT7/PRMT7_WT/Analysis/Cluster/new/PRMT7_WT_aMD_0_300ns.crd.gz
rms first :1-344&!.H=
average crdset cpu-gpu-average
createcrd cpu-gpu-trajectories
crdaction cpu-gpu-trajectories rms ref cpu-gpu-average :1-344&!.H=
crdaction cpu-gpu-trajectories matrix covar \
  name cpu-gpu-covar :1-36&!.H=
runanalysis diagmatrix cpu-gpu-covar out cpu-gpu-evecs.dat \
  vecs 3 name myEvecs \
  nmwiz nmwizvecs 3 nmwizfile dna.nmd nmwizmask :1-36&!.H=
crdaction cpu-gpu-trajectories projection CPU modes myEvecs \
  beg 1 end 3 :1-36&!.H= crdframes 1,last

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


clear all

readdata cpu-gpu-evecs.dat name Evecs

parm /projects/chem/ionic/abhi/PRMT7/PRMT7_WT/Analysis/pca/test-3/PRMT7_WT.prmtop
parmstrip !(:1-344&!.H=)
parmwrite out cpu-gpu-modes.prmtop

runanalysis modes name Evecs trajout \
  pcmin -100 pcmax 100 tmode 1 trajoutmask :1-344&!.H= trajoutfmt netcdf

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Received on Thu Feb 09 2017 - 17:30:03 PST
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