sobolevnrm
commented
1 year ago Hello --
Depending on your force field, this should be the expected behavior (especially with default PDB2PQR settings). The atoms involved in the amino terminus are labeled TER since their parameters are different than the amino group when it is bonded to another amino acid in the peptide chain.
Thanks
I recently used the PDB2PQR webserver to create a pqr file for a protein complex I'm studying. However, when I looked at the pqr file I noticed a handful of residues had been renamed TER, but only a few atoms within each residue.
Here is an example of an Alanine that was altered:
In the original pdb, it was: ATOM 1 N ALA A 1 -26.208 -20.126 3.476 1.00 28.16 N
ATOM 2 H ALA A 1 -26.307 -21.011 3.000 1.00 28.16 H
ATOM 3 H2 ALA A 1 -26.863 -20.097 4.244 1.00 28.16 H
ATOM 4 H3 ALA A 1 -26.421 -19.386 2.824 1.00 28.16 H
ATOM 5 CA ALA A 1 -24.825 -19.995 3.982 1.00 28.16 C
ATOM 6 HA ALA A 1 -24.728 -19.046 4.509 1.00 28.16 H
ATOM 7 C ALA A 1 -23.816 -19.979 2.816 1.00 28.16 C
ATOM 8 CB ALA A 1 -24.561 -21.126 4.990 1.00 28.16 C
ATOM 9 HB1 ALA A 1 -25.288 -21.082 5.801 1.00 28.16 H
ATOM 10 HB2 ALA A 1 -23.564 -21.010 5.415 1.00 28.16 H
ATOM 11 HB3 ALA A 1 -24.627 -22.097 4.499 1.00 28.16 H
ATOM 12 O ALA A 1 -22.928 -20.823 2.773 1.00 28.16 O
But in the pqr it changed to: ATOM 1 N TER A 1 -26.208 -20.126 3.476 -0.3000 1.8500 ATOM 2 CA TER A 1 -24.825 -19.995 3.982 0.2100 2.2750 ATOM 3 C ALA A 1 -23.816 -19.979 2.816 0.5100 2.0000 ATOM 4 CB ALA A 1 -24.561 -21.126 4.990 -0.2700 2.0600 ATOM 5 O ALA A 1 -22.928 -20.823 2.773 -0.5100 1.7000 ATOM 6 HT1 TER A 1 -26.597 -19.218 3.330 0.3300 0.2245 ATOM 7 HA TER A 1 -24.748 -19.129 4.481 0.1000 1.3200 ATOM 8 HB1 ALA A 1 -25.232 -21.071 5.725 0.0900 1.3200 ATOM 9 HB2 ALA A 1 -24.641 -22.004 4.524 0.0900 1.3200 ATOM 10 HB3 ALA A 1 -23.642 -21.023 5.363 0.0900 1.3200 ATOM 11 HT2 TER A 1 -26.200 -20.627 2.612 0.3300 0.2245 ATOM 12 HT3 TER A 1 -26.761 -20.622 4.144 0.3300 0.2245