cartesian_ddg crashes when the mutfile contains multiple mutations to non-canonical residues

Good evening,

I am experiencing an odd behaviour with the cartesian_ddg application (Rosetta version 3.11) when trying to specify multiple simultaneous mutations to non-canonical residues in the mut_file.

All seems to work fine as long as I specify in the mut_file either a single mutation to a non-canonical residue or a mutation to a canonical residue followed by a mutation to a non-canonical residue, but as soon as I try to specify either two mutations to non-canonical residues or a mutation to a canonical residue followed by a mutation to a non-canonical residue I get the following error:

ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.
ERROR:: Exit from: src/core/conformation/Conformation.hh line: 507

[ ERROR ]: Caught exception:


File: src/core/conformation/Conformation.hh:507
[ ERROR ] UtilityExitException
ERROR: Error in core::conformation::Conformation::residue(): The sequence position requested was 0.  Pose numbering starts at 1.

A minimal command to reproduce such behaviour is the following (the PDB file is attached to this post):

$PATH_TO_ROSETTA/main/source/bin/cartesian_ddg.mpi.linuxgccrelease -s relaxed.pdb -ddg:mut_file mut_file.txt -packing:packer_palette:extra_base_type_file ncaalistfile.txt -score:weights ref2015_cart

with mut_file.txt:

total 2
2
V 53 M
L 52 X[DALA]

and ncaalistfile.txt:

DALA

I already double-checked the consistency between the residue numbering in the mut_file and in the PDB file, taking into consideration the fact that my PDB starts from 2.

Has anyone experienced a similar behaviour or has any suggestions for possible workarounds?

Thank you in advance!

Valentina