Files missing in experiment/E3L_6DO3

[zangsk]

Hi,

I successfully ran the examples in benmark without any problems, so I think I installed OpenVS and the required environment correctly. But when running the experiment, problems occurred. I cannot successfully run step 5 in the experiment/README.

Lines 14 and 15 of the script run_dock.vsx.sh are written as follows
*-s ../target/6DO3_0001.lig.pdb
-extra_res_fa ../target/KLHDC2_c8_lig.params *
I found that the folder ‘target/’ is missing. I tried using the 1a30 input file from the benchmark, including complex_1a30_6.pdb and 1a30_ligand.am1bcc.params, but it didn’t work. The error is as follows:

**protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from PDB ../target/6DO3_0001.lig.pdb

ERROR: setup_atomic_charge_reassignments_from_commandline, empty rsd_type_name
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 1786
Error: (0) [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'test_E3L_0_1.6DO3_0001.lig_0001'
Error: (0) [ ERROR ] Treating failure as bad input; canceling similar jobs

[ ERROR ]: Caught exception:

File: src/core/chemical/residue_io.cc:1786
[ ERROR ] UtilityExitException
ERROR: setup_atomic_charge_reassignments_from_commandline, empty rsd_type_name**

Does the 6DO3 used here need any special processing? Could you please upload the files in the folder 'target/' for reference?
Many thanks

[gfzhou]

Thank you for bringing this issue to my attention. I apologize for the missing files; they have now been uploaded to the repository.

[zangsk]

Thank you for bringing this issue to my attention. I apologize for the missing files; they have now been uploaded to the repository.

Thank you for the sample file. I tried to run experiment/E3L_6D03 again, but the error still occurs as follows:

**protocols.jd2.PDBJobInputter: (0) Instantiate PDBJobInputter
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::fill_jobs
protocols.jd2.PDBJobInputter: (0) pushed ../target/6DO3_0001.lig.pdb nstruct index 1
protocols.evaluation.ChiWellRmsdEvaluatorCreator: (0) Evaluation Creator active ...
protocols.jd2.PDBJobInputter: (0) PDBJobInputter::pose_from_job
protocols.jd2.PDBJobInputter: (0) filling pose from PDB ../target/6DO3_0001.lig.pdb

ERROR: setup_atomic_charge_reassignments_from_commandline, empty rsd_type_name
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 1786
Error: (0) [ ERROR ] ERROR: Exception caught by JobDistributor while trying to get pose from job 'E3L_6DO3_0_0.6DO3_0001.lig_0001'
Error: (0) [ ERROR ] Treating failure as bad input; canceling similar jobs

[ ERROR ]: Caught exception:

File: src/core/chemical/residue_io.cc:1786
[ ERROR ] UtilityExitException
ERROR: setup_atomic_charge_reassignments_from_commandline, empty rsd_type_name**

To facilitate testing, I directly used the first line of command in E3L_6DO3_0.cmdlist to run run_dock.vsx.sh. The other steps are the same as in README.
What might be the reason for this kind of error? If the information I provided is not sufficient to describe the problem, please let me know. I would appreciate your reply.