i.e., for some reason, the calculated matrix is a null matrix. I do not think that there is a problem with the generation of the preceding full_no_waters_covar
That's actually the case- I missed two lines in the script I sent you, since what it should read is-
rms ref Crystal_Structure_with_Hydrogens.pdb :38-318&!.H
matrix covar name full_no_waters_covar :38-318&!.H
run
runanalysis diagmatrix full_no_waters_covar out full_no_waters_evecs.dat vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile protein.nmd nmwizmask :38-318&!.H
rms ref Crystal_Structure_with_Hydrogens.pdb :38-318&!.H
projection evecs myEvecsut PCA.project.dat beg 1 end 3 :38-318&!.H
What happened is that since the run command wasn't there after the matrix command, there's a null variable since the command never was executed, and presumably stored in memory. But if you wanted to ever check on the matrix itself then you can do so with-
matrix covar name full_no_waters_covar :38-318&!.H out test.dat
Best,
Kenneth
________________________________
From: Robert Molt <rwmolt07.gmail.com>
Sent: Monday, August 13, 2018 9:07:24 PM
To: amber.ambermd.org
Subject: Re: [AMBER] # of Coordinates Mismatch in PCA
Good evening,
Dr. Huang, I sincerely appreciate your help in this matter. I was hoping
to trouble you further, as I am still encountering an error. I
understand your general diagnosis of the problem, but there still seems
to be a data mismatch.
Everything runs fine up to, but not including, your prescribed line of:
runanalysis diagmatrix full_no_waters_covar out full_no_waters_evecs.dat
vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile
When this line is run in cpptraj, I get the dialogue:
[runanalysis diagmatrix full_no_waters_covar out
full_no_waters_evecs.dat vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile
protein.nmd nmwizmask :38-318&!.H]
Mask [:38-318&!.H] corresponds to 3661 atoms.
nmwiz topology 'piggy.prmtop', 3661 atoms, 244 res, box:
Orthogonal, 0 mol
Changed DataFile 'full_no_waters_evecs.dat' type to Evecs file
for set myEvecs
DIAGMATRIX: Diagonalizing matrix full_no_waters_covar and writing
modes to full_no_waters_evecs.dat
Calculating 3 eigenvectors
Writing 3 modes to NMWiz file protein.nmd
Storing modes with name: myEvecs
Warning: Specified # of eigenvalues to calc (3) > matrix dimension (0).
Warning: Only calculating 0 eigenvalues.
** On entry to DSPEV parameter number 7 had an illegal value
i.e., for some reason, the calculated matrix is a null matrix
On 8/12/18 11:21 PM, Kenneth Huang wrote:
> Hi,
>
>
> I think the problem might becoming up from the datasets that it's calling on-
>
>
> crdaction full_no_waters.mdcrd projection full_no_waters_projection3 modes myEvecs beg 1 end 3 :38-318&!.H=
>
>
> Looks like it's trying to call on the original trajectory that isn't modified to fit what the evecs file is based off of (:38-318&!.H=)- you can check by seeing if the prmtop total number of atoms is the same as 10983.
>
>
> Try this instead- it should be the same thing, but without the crdaction parts:
>
>
> trajin full_no_waters.mdcrd
> reference Crystal_Structure_with_Hydrogens.pdb
> rms ref Crystal_Structure_with_Hydrogens.pdb :38-318&!.H
> matrix covar name full_no_waters_covar :38-318&!.H
> runanalysis diagmatrix full_no_waters_covar out full_no_waters_evecs.dat vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile protein.nmd nmwizmask :38-318&!.H
> projection evecs myEvecsut PCA.project.dat beg 1 end 3 :38-318&!.H
> run
> quit
>
> Best,
>
> Kenneth
>
> ________________________________
> From: Robert Molt <rwmolt07.gmail.com>
> Sent: Sunday, August 12, 2018 1:04 AM
> To: AMBER Mailing List
> Subject: [AMBER] # of Coordinates Mismatch in PCA
>
> Good morning,
>
> I am attempting to perform a principle component analysis but am
> encountering an unexpected error during the projection step using cpptraj:
>
> Error: number selected coords (5865) != number avg coords (10983) in myEvecs
>
> In short, I am confused how a mismatch could occur. My understanding is
> that if my eigenvectors (myEvecs) come directly from the covariance
> matrix of a given trajectory, no mismatch should be possible (if I have
> consistent masks). I must be confused and seek clarification.
>
> I am using cpptraj v. 15. I am following the tutorial specified on
>
> https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fwww.amber.utah.edu%2FAMBER-workshop%2FLondon-2015%2Fpca%2F&data=02%7C01%7Ckhuang8%40student.gsu.edu%7C4cfb63d1c0b946eaf88e08d6018286b5%7C704d822c358a47849a1649e20b75f941%7C0%7C0%7C636698057445333961&sdata=pheknC%2BNMrK5OaR5fxxKqcV8Goi0GHGYhjJPqf8QEHw%3D&reserved=0
>
> My cpptraj commands are (in blue), with trivial warning messages listed
> (in red):
>
> trajin full_no_waters.mdcrd
> reference Crystal_Structure_with_Hydrogens.pdb
>
> Warning: PDB line length is short (67 chars, expected 80).
> Warning: PDB Crystal_Structure_with_Hydrogens.pdb: Reading frame 2, got
> 711 atoms, expected 4431.
> Warning: Only using frames 1-1
>
> createcrd full_no_waters.mdcrd
> run
> crdaction full_no_waters.mdcrd rms ref
> Crystal_Structure_with_Hydrogens.pdb :38-318&!.H
>
> Warning: Coordinates are being rotated and box coordinates are present.
> Warning: Unit cell vectors are NOT rotated; imaging will not be possible
> Warning: after the RMS-fit is performed.
>
> crdaction full_no_waters.mdcrd matrix covar name full_no_waters_covar
> :38-318&!.H
> runanalysis diagmatrix full_no_waters_covar out full_no_waters_evecs.dat
> vecs 3 name myEvecs nmwiz nmwizvecs 3 nmwizfile protein.nmd nmwizmask
> :38-318&!.H
>
> Up to this point, the warnings listed are trivial and everything seems
> fine. I then give the command
>
> crdaction full_no_waters.mdcrd projection full_no_waters_projection3
> modes myEvecs beg 1 end 3 :38-318&!.H=
>
> Error: number selected coords (5865) != number avg coords (10983) in myEvecs
>
>
> --
> Dr. Robert Molt Jr.
>
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Received on Tue Aug 14 2018 - 13:30:02 PDT
