warning in NMA analysis for PDB ensemble input

[Mahnaz Tehrani]

Hi all,

I would like to do NMA analysis on top of an ensemble of PBD files. I have used the following command lines. It has been finished without any error but there is a waring in output file says” multimodel PDB file detected - using only first frame”

So I need all PDB files to be read not only first frame.

Any help will be appreciated.

Cheers

library(bio3d.core,lib.loc="/home/zahra/R/x86_64-suse-linux-gnu-library/4.0")

library(bio3d.nma,lib.loc="/home/zahra/R/x86_64-suse-linux-gnu-library/4.0")

pdbs <- read.pdb("El222-FMN-Red-Beta-s4.pdb", multi=TRUE)

modes <- nma(pdbs)

plot.nma <- plot(modes, pdb=pdbs, spread=FALSE, col="red", type="l")

print(modes)

---

Output:

pdbs <- read.pdb("El222-FMN-Red-Beta-s4.pdb", multi=TRUE)

modes <- nma(pdbs)

Building Hessian...            Done in 0.083 seconds.

Diagonalizing Hessian...       Done in 0.422 seconds.

Warning messages:

1: In nma.pdb(pdbs) :

multimodel PDB file detected - using only first frame

2: In nma.pdb(pdbs) :

Possible multi-chain structure or missing in-structure residue(s) present

Fluctuations at neighboring positions may be affected.

plot.nma <- plot(modes, pdb=pdbs, spread=FALSE, col="red", type="l")

Warning messages:

1: In plot.window(xlim, ylim, ...) : "pdb" is not a graphical parameter

2: In plot.window(xlim, ylim, ...) : "spread" is not a graphical parameter

3: In plot.xy(xy.coords(x, y), type = type, ...) :

"pdb" is not a graphical parameter

[Xinqiu Yao]

For ensemble NMA, you need to create a pdbs object, not simply a pdb object with multiple models. See the tutorial for more details.

You can try to split the models into multiple PDB files (if the number is not too many). Then, read those files by ‘pdbaln()’ to create a ‘pdbs’.

Hope it may help.

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