Hi OpenMM devs!
I'm currently trying to simulate the amino acid ARG capped with ACE and NME. Following the CHARMM convention, I just included ACE and NME atoms into the ARG single residue. It seems like modeller.addExtraParticles() does not work properly since No template found for residue 1 (ARG).
from openmm.app import *
from openmm import *
from openmm.unit import *
pdb = PDBFile('./test.pdb')
forcefield = ForceField('charmm_polar_2019.xml')
modeller = Modeller(pdb.topology, pdb.positions)
modeller.addExtraParticles(forcefield)
I think the input topology is defined correctly. Is there any problem regarding modeller.addExtraParticles() for patch residues? For instance, I've checked that such function correctly added the drude particles for standard residues. There were some issues regarding disulfide patch in CHARMM-Drude 2019 (as seen in #2848) but idk this is also the case. I installed OpenMM 7.7 via source compile and below is the test.pdb file I've used. All bonds (including ARG) are defined.
REARGK 1 CREATED WITH OPENMM 7.7, 2022-10-23
CRYST1 39.352 42.600 80.000 90.00 90.00 90.00 P 1 1
HETATM 1 CH3 ARG A 1 12.588 0.951 34.637 1.00 0.00 C
HETATM 2 H1 ARG A 1 12.260 0.249 35.404 1.00 0.00 H
HETATM 3 H2 ARG A 1 13.545 0.625 34.232 1.00 0.00 H
HETATM 4 H3 ARG A 1 11.848 0.986 33.838 1.00 0.00 H
HETATM 5 CF ARG A 1 12.740 2.325 35.246 1.00 0.00 C
HETATM 6 OF ARG A 1 12.533 2.493 36.449 1.00 0.00 O
HETATM 7 N ARG A 1 13.123 3.308 34.425 1.00 0.00 N
HETATM 8 H ARG A 1 13.287 3.070 33.458 1.00 0.00 H
HETATM 9 CA ARG A 1 13.320 4.724 34.793 1.00 0.00 C
HETATM 10 HA ARG A 1 12.513 5.017 35.464 1.00 0.00 H
HETATM 11 CB ARG A 1 14.696 4.870 35.487 1.00 0.00 C
HETATM 12 HB2 ARG A 1 15.464 5.019 34.729 1.00 0.00 H
HETATM 13 HB3 ARG A 1 14.948 3.936 35.989 1.00 0.00 H
HETATM 14 CG ARG A 1 14.814 5.995 36.536 1.00 0.00 C
HETATM 15 HG2 ARG A 1 15.799 5.913 36.994 1.00 0.00 H
HETATM 16 HG3 ARG A 1 14.768 6.962 36.034 1.00 0.00 H
HETATM 17 CD ARG A 1 13.761 5.964 37.662 1.00 0.00 C
HETATM 18 HD2 ARG A 1 12.850 6.442 37.301 1.00 0.00 H
HETATM 19 HD3 ARG A 1 14.124 6.550 38.506 1.00 0.00 H
HETATM 20 NE ARG A 1 13.423 4.587 38.070 1.00 0.00 N
HETATM 21 HE ARG A 1 12.989 4.012 37.361 1.00 0.00 H
HETATM 22 CZ ARG A 1 13.671 3.938 39.187 1.00 0.00 C
HETATM 23 NH1 ARG A 1 14.257 4.485 40.215 1.00 0.00 N
HETATM 24 HH11 ARG A 1 14.531 5.456 40.162 1.00 0.00 H
HETATM 25 HH12 ARG A 1 14.433 3.947 41.052 1.00 0.00 H
HETATM 26 NH2 ARG A 1 13.319 2.689 39.256 1.00 0.00 N
HETATM 27 HH21 ARG A 1 12.899 2.273 38.436 1.00 0.00 H
HETATM 28 HH22 ARG A 1 13.475 2.139 40.089 1.00 0.00 H
HETATM 29 C ARG A 1 13.248 5.598 33.528 1.00 0.00 C
HETATM 30 O ARG A 1 13.734 5.174 32.490 1.00 0.00 O
HETATM 31 NJ ARG A 1 12.675 6.804 33.549 1.00 0.00 N
HETATM 32 HJ ARG A 1 12.710 7.284 32.661 1.00 0.00 H
HETATM 33 CJ ARG A 1 11.950 7.456 34.640 1.00 0.00 C
HETATM 34 HJ1 ARG A 1 12.642 7.785 35.416 1.00 0.00 H
HETATM 35 HJ2 ARG A 1 11.204 6.784 35.063 1.00 0.00 H
HETATM 36 HJ3 ARG A 1 11.432 8.334 34.254 1.00 0.00 H
TER 37 ARG A 1
CONECT 1 2 3 4 5
CONECT 2 1
CONECT 3 1
CONECT 4 1
CONECT 5 1 6 7
CONECT 6 5
CONECT 7 8 9 5
CONECT 8 7
CONECT 9 7 10 11 29
CONECT 10 9
CONECT 11 12 13 9 14
CONECT 12 11
CONECT 13 11
CONECT 14 15 16 11 17
CONECT 15 14
CONECT 16 14
CONECT 17 18 19 14 20
CONECT 18 17
CONECT 19 17
CONECT 20 21 17 22
CONECT 21 20
CONECT 22 20 23 26
CONECT 23 24 25 22
CONECT 24 23
CONECT 25 23
CONECT 26 27 28 22
CONECT 27 26
CONECT 28 26
CONECT 29 9 30 31
CONECT 30 29
CONECT 31 32 33 29
CONECT 32 31
CONECT 33 34 35 36 31
CONECT 34 33
CONECT 35 33
CONECT 36 33
END
Hi OpenMM devs!
I'm currently trying to simulate the amino acid ARG capped with ACE and NME. Following the CHARMM convention, I just included ACE and NME atoms into the ARG single residue. It seems like
modeller.addExtraParticles()does not work properly since No template found for residue 1 (ARG).I think the input topology is defined correctly. Is there any problem regarding
modeller.addExtraParticles()for patch residues? For instance, I've checked that such function correctly added the drude particles for standard residues. There were some issues regarding disulfide patch in CHARMM-Drude 2019 (as seen in #2848) but idk this is also the case. I installed OpenMM 7.7 via source compile and below is the test.pdb file I've used. All bonds (including ARG) are defined.