[gmx-users] Error in creating parameter files using SwissParam

[GAYATHRI S]

Dear GROMACS users and developers,

I want to run MD simulation of a protein bound to FAD using CHARMM36 force
field. However, I need to generate the parameter files of FAD first.
Hence, I followed the following steps:

1.	Downloaded the .pdb structure file from RCSB PDB databank
2.	Kept the coordinates of FAD and deleted the rest
3.	Added H-atoms and converted to .mol2 file using UCSF Chimera (as
suggested in the website)
4.	Submitted this file as input in the SwissParam site

Error obtained

Thank you for using SwissParam.

Unfortunately, topology and parameters were not successfully generated for
3w2g_fad.
A failure report can be found below.

Failure report:

Possible problem with molecular topology in 3w2g_fad.mol2.
SwissParam will try to reconstruct the topology from coordinates only.


Topology and parameters were NOT generated. Please check the validity of
your molecule.
- Are all hydrogens present in the mol2 file?
- Is the mol2 file correct? Please, read "How to obtain a correct mol2
file?" in the www.swissparam.ch website.

Kindly suggest how I can resolve the issue.

Thank you.

Regards,
Gayathri S