BUG?: nma.pdbs with non-default force field

[Xinqiu Yao]

library(bio3d)
attach(transducin)
modes <- nma.pdbs(pdbs, fit=TRUE, full=TRUE, rm.gaps=TRUE, ff="sdenm")
#Error in eigen(H, symmetric = TRUE) : infinite or missing values in 'x'

Btw, I found that sometimes the coupling of neighboring residues predicted by the default (calpha) force field can be very weak, causing unexpected broken in the correlation network between nodes connected by protein chain. I also found ff "sdenm" generally predicts stronger coupling for neighboring residues, and so I would like to test it on the network analysis.

[Lars Skjærven]

hmm.. any non-standard residues in there? sdENM has the limitation that it's only parameterized for the standard residues...

[Xinqiu Yao]

Right. One structure has "MSE". I will correct the name and try it again. Thanks!

[Lars Skjærven]

you're right. it is abug. looking into it now. but in addition you need standard amino acid identifiers

[Xinqiu Yao]

I corrected but error is still there...

aa <- c("A","C","D","E","F","G","H","I","K","L","M","N","P","Q","R","S","T","V","W","Y")
all(pdbs$ali[!is.gap(pdbs$ali)] %in% aa)
#[1] TRUE
all(pdbs$resid[!is.gap(pdbs$resid)] %in% aa123(aa))
#[1] TRUE

modes <- nma.pdbs(pdbs, fit=TRUE, full=TRUE, rm.gaps=TRUE, ff="sdenm")
#Error in eigen(H, symmetric = TRUE) : infinite or missing values in 'x'

Any idea?

[Lars Skjærven]

I pushed a fix for load.enmff.R now. somehow this was only a problem when rm.gaps=T used through pdbs.nma().

[Xinqiu Yao]

Yes, it is error only with rm.gaps=TRUE. Any way to fix it? Since I still get error after updating to the latest commit of bio3d:

modes <- nma.pdbs(pdbs, fit=TRUE, full=TRUE, rm.gaps=TRUE, ff="sdenm")
Error in solve.default(hess[inds.exc.xyz, inds.exc.xyz]) : 
  system is computationally singular: reciprocal condition number = 5.39083e-21

[Lars Skjærven]

Found the real bug this time :) try again please. The error occurred since I forgot to send the protein sequence to build.hessian from within nma.pdbs.

[Xinqiu Yao]

It works now. Thanks!

[Xinqiu Yao]

Resolved!