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 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.