Closed andrewsb8 closed 8 months ago
Found a new one:
./drop -f setDihedral -n 2 -d phi -i example_files/GLY_connect_110.pdb -o output.pdb -e pdb -c 1 -a 159
Error: File extension for output not recognized.
The commonality between them all is that the input (-i
) has to be first for it to work. For example:
/drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d phi -a 159 -o output.pdb -e pdb -c 1
Writing single-structure pdb file.
The above example works fine.
Now error if angle has a decimal where the -d
option adopts some garbage output.
brian@Research-2022:~/projects/DROP$ ./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 103.2 -o output.pdb -e pdb
Error: dihedral angle chi1������Y@� in residue number 2 was not found.
brian@Research-2022:~/projects/DROP$ ./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi2 -a 103.2 -o output.pdb -e pdb
Error: dihedral angle chi2������Y@�Ӛ�� in residue number 2 was not found.`
The following works:
./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d phi -a 103.2 -o output.pdb -e pdb
Writing single-structure pdb file.
Issue is related to identifying which dihedral needs to rotate (
identifyDihedral
). Different inputs lead to different results:./drop -f setDihedral -a 159 -i example_files/ILE_conect_110.pdb -n 2
Output:
args.res_number: 2, args.dih_type: 2
Expected output:args.res_number: 2, args.dih_type: phi
./drop -f setDihedral -a 159 -i example_files/ILE_conect_110.pdb -n 2 -d psi
Output:
args.res_number: 2, args.dih_type: psi Writing single-structure xyz file. Completed XYZ structure generation. Filename: output.xyz.
In this case, from the output log file
drop.log
, the angle from -a is not recorded.In particular, some command line options are being completely overwritten.