Hi,
I am attempting to use the cpptraj script described in the paper:
"Evaluation of Enhanced Sampling Provided by Accelerated
Molecular Dynamics with Hamiltonian Replica Exchange Methods
Daniel R. Roe, Christina Bergonzo, and Thomas E. Cheatham, III"
I am essentially using the same script as described in the supplemental
info, modified for my system.
I believe the script is getting stuck at the command:
crdaction crd1 projection T1 modes evecs.dat beg 1 end 20 :1-164&!.N,CA,C= \
crdframes 568,10566 out T1.dat
Stating that " Error: Modes should be read in prior to this command with
'readdata' "
That being said, I am not sure where said modes are to be called from. I
thought those were generated by the ccptraj script.
ANy insight would be appreciated.
note: running
AmberTools version 14.07
Amber version 14.03
here is the script I am using:
parm dimer.prmtop
trajin prod01-dimer.mdcrd
trajin prod02-dimer.mdcrd
trajin prod03-dimer.mdcrd
trajin prod04-dimer.mdcrd
autoimage
rms first :1-164&!.N,CA,C=
average dimerAVG.rst restart
createcrd crd1
run
reference dimerAVG.rst.1 [avg]
crdaction crd1 rms ref [avg] :1-164&!.N,CA,C=
crdaction crd1 matrix covar :1-164&!.N,CA,C= name dimerCovar
runanalysis diagmatrix dimerCovar out evecs.dat vecs 20
crdaction crd1 projection T1 modes evecs.dat beg 1 end 20 :1-164&!.N,CA,C= \
crdframes 568,10566 out T1.dat
crdaction crd1 projection T2 modes evecs.dat beg 1 end 20 :1-164&!.N,CA,C= \
crdframes 10568,20566 out T2.dat
crdaction crd1 projection T3 modes evecs.dat beg 1 end 20 :1-164&!.N,CA,C= \
crdframes 20568,30566 out T3.dat
crdaction crd1 projection T4 modes evecs.dat beg 1 end 20 :1-164&!.N,CA,C= \
crdframes 30568,40566 out T4.dat
kde T1:1 kldiv T2:1 klout KL-PC.agr bins 400 name MD-1
kde T1:2 kldiv T2:2 klout KL-PC.agr bins 400 name MD-2
kde T1:3 kldiv T2:3 klout KL-PC.agr bins 400 name MD-3
kde T1:4 kldiv T2:4 klout KL-PC.agr bins 400 name MD-4
kde T1:1 out kde-PC.agr bins 400 name KDE1-1
kde T1:2 out kde-PC.agr bins 400 name KDE1-2
hist T1:1,*,*,*,200 out pca.hist.agr normint name HIST1-1
hist T2:1,*,*,*,200 out pca.hist.agr normint name HIST1-2
run
quit
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Received on Fri Aug 08 2014 - 09:30:02 PDT
