Error in loading pdb files locally

[hema latha]

Hello Lars, I am trying to load the pdb files locally from my computer. One pdb file is crystal structure already downloaded from PDB database, and another one is modelled pdb file. Therefore, I would like to load both of them and align using pdbaln function. Both the pdb files exits in the working directory. But when I am trying to load them locally, I am getting the following error

files<-list.files (".*\.pdb$", full.names=TRUE)

pdbs <- pdbaln(files) Reading PDB files: Error in if (substr(file, 1, 4) == "http") { : missing value where TRUE/FALSE needed

Please help in resolving this issue.

Thank you in advance.

[Barry Grant]

Looks like your list.files() call is not working properly. I suggest you look at its output.

Also can you not just try to write out the files names you are after like so:

myfiles = c("1BG2.pdb", "model.pdb")
pdbs = pdbaln(myfiles)

[hema latha]

Hi Barry, Thank you for the answer. I could able to load the pdb files locally.
Is it possible to generate .dcd files for the modelled pdb files in bio3d? if so, how can I do that? Please let me know.

Thank you.

[Barry Grant]

I don't know what you are asking for here. DCD and related (but in my opinion better) NetCDF files are typically from simulations and the like. Do you want to just combine both your input structures into an output trajectory file or do you want to run some type of simulation?

[hema latha]

Hi Barry, As you have mentioned, I want to combine both of input structures i.e. crystal structure + model.pdb into an output trajectory file and want to produce output files like RMSD, RMSIF, PCA plots and other analysis of my project. Like, I want to compare the model.pdb with that of crystal structure and want to see the differences between both of them.

[Barry Grant]

I suggest you read the various online tutorials where these things are explained in some detail.

In particular, you might like to start with the 'Coordinate superposition and structural alignment' and 'Working with multiple PDB files' sections of http://thegrantlab.org/bio3d/tutorials/structure-analysis and then work your way through other tutorials as necessary.