D'oh!!!
Thank you, Jason. I am an idiot to have not seen that! This is what I
get for being new to masks.
Dr. Huang, I am also still attempting your method as well.
On 8/14/18 7:55 PM, Jason Swails wrote:
>
>
>> On Aug 12, 2018, at 1:04 AM, Robert Molt <rwmolt07.gmail.com> wrote:
>>
>> 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
>>
>> http://www.amber.utah.edu/AMBER-workshop/London-2015/pca/
>>
>> 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
> Note the mask. :38-318&!.H
>
> This selects all atoms in residues 38-318 not including atoms names H.
>
>> crdaction full_no_waters.mdcrd projection full_no_waters_projection3
>> modes myEvecs beg 1 end 3 :38-318&!.H=
> Note this mask with a = at the end. The = is a wildcard that omits all atoms that STARTS with H. This includes a lot more atoms that are excluded from the mask you’re doing the projection on.
>
>> Error: number selected coords (5865) != number avg coords (10983) in myEvecs
> Based on this, there are (10983-5865)/3=1706 atoms that start with H but are not named H.
>
> Make sure you’re using exactly the same mask in each step.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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--
Dr. Robert Molt Jr.
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Received on Tue Aug 14 2018 - 18:30:03 PDT
