I docked one ligand to one protein then I got the best mode of ligand and I combined the ligand best mode to the protein in PDB file. I carried out ONIOM for next step but I got error such as bellow:
Error parsing atomic flags:
QPERR --- A SYNTAX ERROR WAS DETECTED IN THE INPUT LINE.
PDBNAME=N,RESNAME=ALA,RESNUM=4_A
How can I repair the input file so that I do not get error anymore?
Does the error message refer to the command input or the pdb file? it is next to impossible to troubleshoot such error messages without seeing either. A syntax error can be triggered by an error in the command input, or by the data input not conforming to the expectations of the program. Did the program work OK with other pdb files, using the same command input?
If its, the PDB file, we would have to see it, at least the region around residue 4, to see if it in any way deviates from the standard. Does "RESNUM=4_A" stand for residue 4 in chain A, or does residue 4 have an alternative localization? This can trigger errors in some programs.
- Badges
- Science topic
- Similar topics
- Chemistry