Incorporating Ligand into calculations and other errors

Hello,

I too work on the protease and I understand from the vignettes on the site that only CA atoms are used for demonstration. I would like to use the CA atoms and a ligand for my calculations so I have manipulated my trajectory and PDB files to make use of only CA atoms and all ligand atoms. That being said, this is how I read in the files

dcd <- read.dcd("/Users/debraragland/CA_DRV.dcd")
pdb <- read.pdb("/Users/debraragland/CA_DRV.pdb")
inds <- atom.select(pdb, resno = c(24:27, 85:90), elety = "CA", resid = "017", operator = "OR") #the ligand has different atom names in the same column where the CA atoms are listed and 017 in the residue name column, is this properly incorporating the ligand?
trj <- fit.xyz(fixed = pdb$xyz, mobile = dcd, fixed.inds = inds$xyz, mobile.inds = inds$xyz)
cij <- dccm(trj)
net <- cna(cij)

This a sample of protein and ligand atoms from my pdb

ATOM 94 CA GLY A 94 2.008 3.497 16.220 0.00 0.00 C2 C (protein atom)
ATOM 105 O10 017 A1200 -0.766 0.443 -6.205 0.00 0.00 C2 O (ligand atom)

Everything seems to compute fine with no errors until I try;

view.dccm(cij, pdb)

where I get;

Error in view.dccm(cij, pdb) : unequal vector lengths

I have tried the suggestions from other posts here on the bitbucket, however nothing is working for me (Issues 248 and 260).

When I look at

dim(cij)
[1] 236 236

dim(pdb$atom)
[1] 236 16

I don't know how to fix the problem.

If I change the "017" to read as CA, I get the same error, if I change the ligand name to random residues, I get the same error. I can use plot.dccm(cij) just fine. I should note, that I've never encountered an error when superposing with just the CA atoms as in the vignette, am I incorporating the ligand atoms incorrectly?

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