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Dihedral Rotation Of Proteins

License: GNU General Public License v3.0

C 92.59% Shell 6.79% Makefile 0.62%

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Some error in large chi angle rotations between log output and VMD calculations

Below are examples of large errors showing small discrepencies between calculation of dihedral angles after rotation in this code base and with the VMD software suite (https://www.ks.uiuc.edu/Research/vmd/) when rotations are large (~50 degrees). This error does not appear to show for smaller rotations (~4 degrees). Examples are shown below with logs and visualizations with VMD.

Input with error:
./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 159 -o output.pdb -e pdb

Output log:

Command Line: ./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 159 -o output.pdb -e pdb

Reading structure file: example_files/ILE_conect_110.pdb

Not printing covalent bond matrix

Number of dihedrals identified in structure: 4
Calculating initial dihedral angles.
Columns: Angle, Angle Type (phi, psi, etc), Residue Name, Residue Number, Dihedral Number
-86.610730 phi ILE 2 0
165.397344 psi ILE 2 1
99.733809 chi1 ILE 2 2
-71.905838 chi2 ILE 2 3

Done reading structure file: example_files/ILE_conect_110.pdb

Found dihedral number: 2

Changing dihedral angle chi1 in residue number 2 by 59.266191 degrees.

Rotation complete. Please check the accuracy of the operation.
User input angle: 159.000000
Angle after rotation: 159.000000

VMD dihedral:

Input without error:
./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 103 -o output.pdb -e pdb

Output log:

Command Line: ./drop -f setDihedral -i example_files/ILE_conect_110.pdb -n 2 -d chi1 -a 103 -o output.pdb -e pdb

Reading structure file: example_files/ILE_conect_110.pdb

Not printing covalent bond matrix

Number of dihedrals identified in structure: 4
Calculating initial dihedral angles.
Columns: Angle, Angle Type (phi, psi, etc), Residue Name, Residue Number, Dihedral Number
-86.610730 phi ILE 2 0
165.397344 psi ILE 2 1
99.733809 chi1 ILE 2 2
-71.905838 chi2 ILE 2 3

Done reading structure file: example_files/ILE_conect_110.pdb

Found dihedral number: 2

Changing dihedral angle chi1 in residue number 2 by 3.266191 degrees.

Rotation complete. Please check the accuracy of the operation.
User input angle: 103.000000
Angle after rotation: 103.000000

VMD dihedral:

Large pdb files lead to seg fault

Seg fault, with no log outputs, is the result when using -i examples/Villin-Headpiece/villin-unfolded-conect.pdb as an input file. Can be a memory leak or need to test on system with more system memory.

command line inputs are not working correctly in ```setDihedral```

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.

Number of dihedrals identified in structure: 4
Calculating initial dihedral angles.
Columns: Angle, Angle Type (phi, psi, etc), Residue Name, Residue>
-86.610730 phi ILE 2 0
165.397344 psi ILE 2 1
99.733809  ILE 2 2
-71.905838  ILE 2 3

Done reading structure file: example_files/ILE_conect_110.pdb

Found dihedral number: 1

Changing dihedral angle psi in residue number 2 by -165.397344 de>

Rotation complete. Please check the accuracy of the operation.
User input angle: 0.000000
Angle after rotation: -0.000000

In particular, some command line options are being completely overwritten.

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