- marked as task
error_ ensemble NMA
Hi,
I am trying to perform ensemble NMA.
I am getting weird error: "Warning in mylapply(1:length(pdbs$id), .calcAlnModes, pdbs, xyz, gaps.res, : all scheduled cores encountered errors in user code Error in tmp.modes$U : $ operator is invalid for atomic vectors"
code:
pdbs.list <-list.files(path="path",pattern="^pdb_a_")
align.pdbs <- pdbaln(pdbs.list,fit = FALSE)
modes <- nma(align.pdbs,keep = 50, mass = TRUE, ff="calpha", ncore=2, fit=FALSE)
thank you
Comments (7)
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reporter -
Could you provide an example
pdbs
object that we can reproduce your problems? You can either attach the file here or send it to xinqiu.yao@gmail.com. -
reporter Hi Yao,
The problem was ( I think) that I was operating on Calphas only. When I pdbaln whole structures, the problem disappeared. Nevertheless, I encountered another problem.
Error: ... dimension of x$U.subspace: ( 13944x13938x4 ) ... aligned eigenvectors (gap containing positions removed)
... estimated memory usage of final 'eNMA' object: 5931.6 Mb| | 0%Error in modes$U[, k] : subscript out of bounds
I managed to reproduce the problem. The argument, which is causing the problem is: "keep=30". Without it, eNMA goes fine. Nevertheless, I would prefer to store only first 30.. If I store all modes for my protein, the binaries go really big and working with these is quite inconvenient.
The problem appears on two different platforms:
(1) Mac Os, R version 3.4.1 (2017-06-30)
(2) Linux cluster, R version 3.4.2 (2017-09-28)
The code is exactly the same.
pdbs.list <-list.files(path="path",pattern="^pdb_a_") align.pdbs <- pdbaln(pdbs.list,fit = FALSE) modes <- nma(align.pdbs,keep = 30, mass = TRUE, ff="calpha", ncore=2, fit=FALSE)
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Hi,
Instead of using
keep=30
, trysubspace=30
(Seehelp(nma.pdbs)
for more detail).(To Lars: We need to override 'subspace' when users set 'keep' in calling nma.pdbs() (otherwise, 'out of boundary' errors). Or, we can modify to ignore 'keep' in nma.pdbs(). What do you think?)
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reporter Thanks Yao. I will try and I will let you know. cheers
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reporter Worked. Please, close this ticket.
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- changed component to ToDo
- marked as minor
- changed version to v2.3 [devel]
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assigned issue to
(To Lars: We need to override 'subspace' when users set 'keep' in calling nma.pdbs() (otherwise, 'out of boundary' errors). Or, we can modify to ignore 'keep' in nma.pdbs(). What do you think?)
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