Error in CGenFF and CHARMM-GUI While Building Files

User discussions
1

Dear all,

I’m getting an error while generating a .str file of my ligand to be simulated. I have also tried to generate my .mol2 file using several editors like SAMSON, Chimera and Avogadro, then generated ligand_fix.mol2 to upload it but still getting the error from the server.

readmol2 warning: non-unique atoms were renamed.
Now processing molecule LIG ...
resonance warning: unfulfilled valence in aromatic subgraph; skipped molecule

Is there any solution of this problem? My ligand contains several aromatic units and it appears that the problem stems from this. How can I deal with it?

On the other hand, I also tried to build my protein-ligand structure using CHARMM-GUI but it gives me the following error:

Error parsing HETAT, expected chain ID at column 22, but got '':
HETATM 4673  C   LIG     1      28.458  21.426  92.346                       C  
                     ^

Thanks in advance.

2

The first error is that your .mol2 is chemically flawed, either from assignment of atom types or bonds, or both. The second error means you need a chain identifier in the PDB file. You have none.

Neither of these are GROMACS issues, so you should seek help via the CGenFF or CHARMM-GUI developers.

3

AOA
There is an error in generating .str file with sulphur containg ligand. CGENFF server not supporting sulphur atoms then how can I fix that error? Is their any alternate forcefield to be applied ? I am the beginner and it is requested to provide a detailed solution.

ERROR:
readmol2 warning: non-unique atoms were renamed.
Now processing molecule UNK …
attype warning: unknown sulfur type not supported;
skipped molecule.