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No template found for residue 645 (G) and Error on using gromacs inputs #4512
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Did you follow the link in the error message and read the explanation? It describes the possible causes pretty well. |
Yeah I check through the link and tried fixing some issues using PDBFixer, changed some residue names too at last ended up with this issue trying to figure it out. This works good in gromacs using AMBER99SB and AMBER94 forcefield ATOM 10447 P G A 645 184.542 282.747 268.948 1.00 0.00 P The file is ribosome structure 6i0y id ` pdb = PDBFile(test_cif_fixed_pH_7.pdb') forcefield = ForceField('amber14-all.xml', 'amber14/tip3pfb.xml') |
As I am still facing issue in loading Pdb in OpenMM directly And since My pdb is loading perfectly in gromacs, I used the gro and top files as input to the Openmm system, it works from openmm.app import GromacsTopFile, GromacsGroFile, PDBFile, Simulation Load the GROMACS filesgro_file = 'solvated.gro' gro = GromacsGroFile(gro_file) Create the systemsystem = top.createSystem(nonbondedMethod=PME, nonbondedCutoff=1.0*nanometer, constraints=HBonds) make some modifications and delete few water moelcules modeller.delete(list(water_to_delete)) Now how to use the updated modeller to run the simulation as I need to build a updated system to run simulation correct? But I am not able to save in gro or top format to and create updated system. This is raising problem too. |
The chain is terminated incorrectly. The Amber force field expects the phosphate to be missing at the 5' end, replaced with just a hydrogen on O5'. Your file includes both the phosphate and the hydrogen, meaning that you have O5' bonded to three other atoms. |
ValueError: No template found for residue 645 (G). The set of atoms matches G3, but the bonds are different. Perhaps the chain is missing a terminal group? For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#template
May I know how to resolve this issue why is it occurring?
Any help please
test_cif_fixed_pH_7.pdb.zip
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