I've been getting a fairly common error when trying to perform a side-chain refinement:

"Side-Chain Refinement: Atom sequence order has changed please re-type molecule with a forcefield. Failed Side Chain Refinement".  I get this error even for very simple systems (i.e. systems without any HETATMS that may cause issues).

Here's one example:

Open Url -> get 1ENH.pdb

Prepare protein (Build Loops = False; Protonate = True (default settings under this group); Forcefield = CHARMPLR; keep ligands = FALSE, Keep Water=None).

Select all residues

Side-Chain Refinement

If, however, I do the same procedure as above except I use the CHARMm forcefield instead of CHARMPLR, it works fine.

I'd rather work with the CHARMPLR - any ideas how to work around this error?  (Other than protonating with CHARMm -> Side-Chain Refinement -> Remove Hydrogens -> Re-add hydrogens with CHARMPLR).

I'm using Discovery Studio 4.0