Re: [AMBER] PCA

From: Elvis Martis <elvis.martis.bcp.edu.in>
Date: Fri, 10 Feb 2017 01:26:36 +0000

HI,

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

[photo]



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


A Kalina, Santacruz [E], Mumbai 400098, INDIA
W www.elvismartis.in<https://webapp.wisestamp.com/www.elvismartis.in>
Skype. adrian_elvis12<https://webapp.wisestamp.com/#>


[https://ci3.googleusercontent.com/proxy/P0F8-p0kwxKdscp6zsT-ZSRttk9OJEsBGiaXej_H2ERz8n2ma5SLHFAWJdKL-wqOlXSGjbmEyga9C8lmU1bs-_yPIq3CnazA5eJVDYjce1r-34uwxqjjRnmAtE473lEq28nSHQ=s0-d-e1-ft#https://s3.amazonaws.com/images.wisestamp.com/icons_for_colors_32/linkedin.png&retryCount=1]<http://www.linkedin.com/in/elvisadrianmartis/>





________________________________
From: Thakur, Abhishek <axt651.miami.edu>
Sent: 10 February 2017 03:50:48
To: amber.ambermd.org
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
run
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

run

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 cpu-gpu-mode1.nc \
  pcmin -100 pcmax 100 tmode 1 trajoutmask :1-344&!.H= trajoutfmt netcdf

_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 09 2017 - 17:30:03 PST