Hi,
Add 'name evecs.dat' to the 'runanalysis diagmatrix' line. This will
name the modes data set created by diagmatrix to 'evecs.dat' so that
the subsequent 'projection' commands can find it, e.g.:
runanalysis diagmatrix dimerCovar out evecs.dat vecs 20 name evecs.dat
Let me know if that doesn't work for you,
-Dan
On Fri, Aug 8, 2014 at 10:17 AM, Jonathan Gough
<jonathan.d.gough.gmail.com> wrote:
> 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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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 307
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Aug 08 2014 - 10:00:02 PDT
