Dear Rosetta users,
I'm trying to run Rosetta VIP on a heme protein. I started by relaxing the structure according to the protocol in the "relax_around_chemically_bound_ligand" demo. My chemically bound ligand would be the heme group, to a histidine. For this, I created *.params files for the heme group and the covalently bound histidine, and created a contraints file according to the protocol. The relaxation seemed to work fine (log.txt available), as Rosetta was able to make the connection between heme and his and apply the constraints.
The problem is when I try to run Rosetta VIP on the relaxed protein (log file available). I give Rosetta both *.paramas files, the contranints file, a resfile (resfile says "don't touch heme nor his") and the starting structure. My flag file for VIP reads:
-extra_res_fa HEM.params # *.parmas file for HEME
-extra_res_fa HIS.params # *.parmas file for modified HIS
-mute protocols.simple_moves protocols::checkpoint protocols.relax core.scoring.etable basic.io.database core.io.pdb core.chemical protocols.packstat #core.pack
The first problem appears when core.conformation.Conformation attempts to connect the Fe atom from the heme to the N atom from the histidine:
core.conformation.Conformation: Failed to find a residue connection for residue 154 with connection point 1
(residue 154 is the heme)
What surprised me is that core.conformation.Conformation is the same thinf that makes the bond properly in the relax application (this can be seen in the relax log file).
Then, VIP keeps running and I have a second error, which is the following:
core.pack.task.ResfileReader: APOLAR mode read for residue 154 which has been instructed to use non-canonical amino acids.
ERROR:: Exit from: src/core/pack/task/ResfileReader.cc line: 1485
VIP stops running there. The error seems (IMO) to be related to the params file, because I can comment the resfile line in the flag file and nothing changes.
Let me know if you want me to post the complete log file from VIP.