NMA with non-standard residue name
Dear bio3d team,
I am trying to calculate Normal Modes for protein which is labelled at two places.
For Normal Modes Hessian should be mass-weighted so when I code call as:
modes <- nma(pdb, inds=sele,mass=TRUE)
Error in aa2mass(pdb = c("MET", "ASN", "ILE", "PHE", "GLU", "MET", "LEU", : Unknown amino acid identifier: CYR
call fails
when I code call as:
modes <- nma(pdb, inds=sele, mass=FALSE) Building Hessian... Done in 0.026 seconds. Diagonalizing Hessian... Done in 0.073 seconds.
dim(modes$U) [1] 492 492 print(modes)
It works.
If I understand hessian should be mass-weighted.
Is there a way to address this.
Thank you.
Mamta
Comments (5)
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- changed title to NMA with non-standard residue name
- marked as task
- changed version to v2.3 [devel]
- marked as trivial
- changed component to Q&A
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reporter Thank you.
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- changed status to resolved
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reporter Dear Lars,
I am reopening this issue.
I tried both methods as you suggested. But I still have trouble getting the results.
Please take a look at this:
cyr1.mass <- list("CYR1"=264) cyr1.mass $CYR1 [1] 264
nma(pdb, inds=sele, mass.custom=cyr1.mass) Error in aa2mass(pdb = c("MET", "ASN", "ILE", "PHE", "GLU", "MET", "LEU", : must supply 'pdb' object or vector of amino acid residue names aa.table = rbind(aa.table, CYR1=c("CYR1", "C", 264, NA, NA))
Since it was not counting labelled C-alpha so I extracted index as
sele <- atom.select(pdb, elety="CA")
sele
Call: atom.select.pdb(pdb = pdb, elety = "CA")
Atom Indices#: 164 ($atom) XYZ Indices#: 492 ($xyz)
And tried to run nma call. This is what I get.
nma(pdb, inds=sele, mass.custom=cyr1.mass) Error in aa2mass(pdb = c("MET", "ASN", "ILE", "PHE", "GLU", "MET", "LEU", : must supply 'pdb' object or vector of amino acid residue names
After adding mass to aa.table table if I run nma call, it works but it skips CYR1 at both the sites and.
nma(pdb) Building Hessian... Done in 0.044 seconds. Diagonalizing Hessian... Done in 0.061 seconds.
Call: nma.pdb(pdb = pdb)
Class: VibrationalModes (nma)
Number of modes: 486 (6 trivial)
Frequencies: Mode 7: 0.013 Mode 8: 0.013 Mode 9: 0.015 Mode 10: 0.021 Mode 11: 0.024 Mode 12: 0.027
- attr: modes, frequencies, force.constants, fluctuations, U, L, xyz, mass, temp, triv.modes, natoms, call Warning message: In nma.pdb(pdb) : Possible multi-chain structure or missing in-structure residue(s) present Fluctuations at neighboring positions may be affected.
I would appreciate your help.
Mamta
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Yes- the mass of residue CYR is unknown. You can either add CYR to the
aa.table
data frame and then runnma()
or you can the argumentmass.custom
:Hope it helps. L