Errors in Reading PDB File

[Olivia Debnath]

Hey! For my research, I need to do some in-silico mutagenesis (for example, mutating phenylalanine to alanine) using the PDB structure. I did the mutation using PyMol Mutagenesis Wizard and then did the energy minimization using Force Field: OPLS 2005. Now, I want to use this PDB file to do CNA in bio3d- mainly to see how the community nodes are reorganized. The problem is bio3d is showing errors in reading the file:

setwd("Documents") pdb <- read.pdb("filename.pdb") Error in .read_pdb(file, multi = multi, hex = hex, maxlines = maxlines, : basic_string::substr

The energy optimized file is attached herewith- W165C_Opt.pdb.

[Xinqiu Yao]

Hi,

Thanks for reporting. We will check the error soon. At the same time, you can use read.pdb2(), which works fine in my test.

[Barry Grant]

See also #542 related to the new read.pdb() vs the old read.pdb2() function.

[Xinqiu Yao]

Fixed by the latest commit.