Closed iliqKichev closed 1 year ago
I don't think this is a problem with pdb2dat
. Your .pdb
file is formatted differently from what it normally expects. If you run pdb2dat
without any options, it tells you it will look from the coordinates starting from column 6. In your .pdb
file they coordinates start in column 5 -- because you don't have the residue name column in your file.
To fix the problem just pass -f 5
-- it will ask the script to start looking for coordinates in column 5 rather than the default 6.
When there is a planar molecule and the padding option is used, the lattice size in the output file in the planar dimension is set to a large negative number.
Example file: BQ.pdb
Command: BQ.dat
pdb2dat -a -m -w -x 9 -y 9 -z 9 BQ.pdb
Output: