Hello everyone,

I am trying to prepare a protein that I received which was refined. The issue is that when I try to prepare a topology file on GROMACS, I get the following error:

Fatal error:

Residue 129 named GLU of a molecule in the input file was mapped

to an entry in the topology database, but the atom CG used in

that entry is not found in the input file. Perhaps your atom

and/or residue naming needs to be fixed.

And then when using the same protein in Chimera, I get this error:

Residue #0:134.A (GLU/glutamic_acid) should have either atom HB1 or HB3, but not both You must specify a formula

I thought maybe minimizing the energy of the protein would be helpful, but I see that Chimera can add/edit the protein. I know that there are some incomplete side chains on the protein.

I complete them, would it essentially produce a protein not the same as the protein of interest? Also, how would I fix the CG atom not being found in the input file?

If anyone would know anything about this, please advise.