Reading PDB file from local disk

[Former user]

I try to read the file from a local disk: The commands given are:

library(bio3d) setwd("/home/prasanth/GNM/AURKA/GNM/Free/") pdb <- pdb.read("4j8n") pdb <- read.pdb("4j8n")

Warning message: In get.pdb(file, path = tempdir(), verbose = FALSE) : /tmp/RtmpzUUPyz/4j8n.pdb exists. Skipping download

I believe that this warning is due to the presence of a preexisted file. How can I read the file from a local disk without any error.

Please also note that command which incorporates system.file DOESNT work for me. pdb <- read.pdb( system.file("/home/prasanth/GNM/AURKA/GNM/Free/4j8n", package="bio3d") ) Error in read.pdb(system.file("/home/prasanth/GNM/AURKA/GNM/Free/4j8n", : No input PDB file found: check filename

[Lars Skjærven]

please keep only one thread per issue