@hess
@jalemkul
Hello,
I hope this email finds you well.
I used a MOL2 file as input in CHARMM-GUI to generate the .rtp file for a non-standard residue in GROMACS.
I then used pdb2gmx to generate the topology for this residue. Later, I noticed that the bonds in the MOL2 file were not listed in ascending order.
I didn’t receive any errors about the bond order or mismatches between the topology and the gro file.
Because it’s an RTP file, we only have the charges, and it seems this should not cause any problems.
I would like to confirm: Could the unordered bonds in the MOL2 file impact the accuracy of the topology or simulation? Or is this not a concern in this case?
I want to ensure that my simulation results remain reliable.
Thanks for your help!
Best regards,
Fatemeh,