Hey all,
I've found an issue in my .prmtop file that is caused by creating a bond in tleap between a protein and its heme. I've found some threads on here that suggest using checkValidity and setMolecules in parmed to repair the topology file, but when I do that, I get the following error:
> checkValidity
Determining validity of prmtop
1 total warnings
ParmWarning: ATOMS_PER_MOLECULE section corrupt! Molecules are not contiguous!
> setMolecules
Setting MOLECULE properties of the prmtop (SOLVENT_POINTERS and ATOMS_PER_MOLECULE)
AmberWarning: Molecule atoms are not contiguous! I am attempting to reorder the atoms to fix this.
AmberWarning: Residues cannot be part of 2 molecules! Molecule section will not be correctly set. [Offending residue is 497: <Residue HEM[497]>]
I've also tried repairing it with fixatomorder in cpptraj. It runs with no errors, but when I run checkValidity on the topology file output by cpptraj, I still get the same set of warnings.
All suggestions welcome,
Sam Ratliff
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Received on Thu Aug 06 2020 - 10:30:02 PDT
