No template found issue for C-terminal residues about openmm

[peastman]

Your PDB file has some problems. Here's the relevant section.

ATOM   3180  N   LEU A 208      16.948   7.178 -25.739  1.00  0.00           N  
ATOM   3181  CA  LEU A 208      16.310   8.466 -25.974  1.00  0.00           C  
ATOM   3182  C   LEU A 208      16.648   9.279 -24.730  1.00  0.00           C  
ATOM   3183  O   LEU A 208      16.170  10.374 -24.556  1.00  0.00           O  
ATOM   3184  CB  LEU A 208      14.753   8.364 -26.231  1.00  0.00           C  
ATOM   3185  CG  LEU A 208      13.752   7.984 -25.121  1.00  0.00           C  
ATOM   3186  CD1 LEU A 208      12.210   8.109 -25.515  1.00  0.00           C  
ATOM   3187  CD2 LEU A 208      14.057   6.586 -24.499  1.00  0.00           C  
ATOM   3188  OXT LEU A 208      17.557   8.801 -23.735  1.00  0.00           O1-
ATOM   3189  H   LEU A 208      17.135   7.052 -24.755  1.00  0.00           H  
ATOM   3190  HA  LEU A 208      16.620   8.874 -26.937  1.00  0.00           H  
ATOM   3191  HB2 LEU A 208      14.416   9.385 -26.406  1.00  0.00           H  
ATOM   3192  HB3 LEU A 208      14.541   7.805 -27.142  1.00  0.00           H  
ATOM   3193  HG  LEU A 208      13.901   8.670 -24.287  1.00  0.00           H  
ATOM   3194 HD11 LEU A 208      11.802   9.060 -25.173  1.00  0.00           H  
ATOM   3195 HD12 LEU A 208      11.996   8.144 -26.583  1.00  0.00           H  
ATOM   3196 HD13 LEU A 208      11.586   7.305 -25.125  1.00  0.00           H  
ATOM   3197 HD21 LEU A 208      14.381   5.925 -25.303  1.00  0.00           H  
ATOM   3198 HD22 LEU A 208      14.820   6.631 -23.722  1.00  0.00           H  
ATOM   3199 HD23 LEU A 208      13.164   6.208 -24.001  1.00  0.00           H  
ATOM   3200  N   GLU A 219       9.932   6.197 -38.597  1.00  0.00           N  
ATOM   3201  CA  GLU A 219      10.440   6.597 -37.279  1.00  0.00           C  
ATOM   3202  C   GLU A 219       9.540   6.216 -36.004  1.00  0.00           C  

Some things to notice here.

• The residue ID jumps from 208 to 219, suggesting there are probably some missing residues.
• There's a big gap in space. Atom C of LEU 208 and atom N for GLU 219 are close to 20 A apart. That also suggests there are missing residues, and those atoms should be bonded together as a single chain.
• The LEU has been terminated as if it were the end of a chain. It contains an OXT atom, which is only found in C-terminal residues.
• But contrary to all of the above, it's all one chain. There's no TER record to indicate a new chain, and the chain ID remains unchanged as A.

[okbckim]

Thank you so much for your comprehensive comments.

I changed Chain ID from A to B or C when missing loops exist. With this simple change as you suggested, I am able to run the simulation. Great suggestion!

[peastman]

Glad that worked!

[okbckim]

Can I ask you one more question related to the subject.
I call modeller.addMembrane to add POPC membrane. I was able to run the simulation with the system.
Then, I built membrane using another software. The POPC molecule looked same except coordinates. However, I encountered the error message. 284 POP is the first POPC molecule in the system.

ValueError: No template found for residue 284 (POP). The set of atoms matches POPC, but the bonds are different. Perhaps the chain is missing a terminal group? I attached the pdb file from this case.

Thank you again!
system.pdb.txt

[peastman]

The file is missing CONECT records. This is discussed in the FAQ entry linked in the error message.

[okbckim]

Thank you again for the insight. My bad. I will add CONECT section as you suggested.