On Mon, Aug 20, 2018 at 4:50 PM, Robert Molt <rwmolt07.gmail.com> wrote:
> Good afternoon,
>
> It seems I have been two steps forward, one step back on this problem. I
> am still encountering an error in matching the dimensionality of the
> matrices. I believe that my masks are now perfectly consistent with one
> another, unlike the preceding error. The error occurs only in the last
> step of the below-listed ptraj script. The script is written in blue,
> the ptraj output written in green.
>
> parm piggy.prmtop
> trajin full_no_waters.mdcrd 1 last 100
> reference Crystal_Structure_with_Hydrogens.pdb
> createcrd full_no_waters.mdcrd
> run
> crdaction full_no_waters.mdcrd rms ref
> Crystal_Structure_with_Hydrogens.pdb :38-318&!.H=
> 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=
> crdaction full_no_waters.mdcrd projection full_no_waters_projection3
> modes myEvecs beg 1 end 1 :38-318&!.H=
> clear all
> readdata full_no_waters_evecs.dat name Evecs
> parm piggy.prmtop
> parmstrip !(:38-318&!.H=)
>
> Up to this point, ptraj output clearly specifies that there are 1955
> atoms after the mask, 2476 before. There are no errors. Here is the
> specific text justifying my words:
>
> [parmstrip !(:38-318&!.H=)]
> Stripping atoms in mask [!(:38-318&!.H*)] (2476) from piggy.prmtop
> Stripped parm: 1955 atoms, 244 res, box: Orthogonal, 1 mol
>
You have stripped out residues 1-37 and 319-<total number of residues>.
You now have 244 residues left (it seems that your system doesn't have 318
full residues? I would have expected 281 left if it did). These are now
residues 1-244 since cpptraj always numbers residues from 1.
parmwrite out cpu-gpu-mode1.prmtop
> runanalysis modes name Evecs trajout cpu-gpu-mode1.nc \
> pcmin -100 pcmax 100 tmode 1 trajoutmask :38-318&!.H= trajoutfmt netcdf
>
> At this point, I get the error:
>
> [runanalysis modes name Evecs trajout cpu-gpu-mode1.nc pcmin -100
> pcmax 100 tmode 1 trajoutmask :38-318&!.H= trajoutfmt netcdf]
> Mask [:38-318&!.H*] corresponds to 1653 atoms.
>
Mask :38-318&!.H= now applies to the stripped system, and selects only
residues 38 - 244, effectively skipping the first 37 residues altogether.
Those first 37 residues clearly had 1955 - 1653 = 302 non-hydrogen atoms
among them (seems about right for amino acid heavy atoms).
Once you do the parmstrip, you want to keep *all* of the remaining atoms
when projecting onto the stored eigenmodes.
HTH,
Jason
--
Jason M. Swails
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Received on Mon Aug 20 2018 - 20:00:02 PDT
