Hello
I am trying to minimze a structure using the minimize_with_cst script.
However, I keep getting the error message:
ERROR: Cannot open file "ATOM"
Based on this thread , I thoghout that I should use the in:file:s option instead of in:file:l which is recoomende in the ddg_monomer documenation, but I still get this error.
The error presist wheter I pass the list of pdbs as a variable, or pass a file that containts the names of the PDB files (as suggetsed here) but I invaribly get this error.
The command that I am passing is:
/path/to/minimize_with_cst.linuxgccrelease -in:file:l $pdbs_to_minimize <I also tried this with -in:file:s> -in:file:fullatom -ignore_unrecognized_res -fa_max_dis 9.0 -database $ROSETTA_DB -ddg::harmonic_ca_tether 0.5 - -ddg::constraint_weight 1.0 -ddg::out_pdb_prefix min_cst_0.5 -ddg::sc_min_only false -beta_nov15 > mincst.log
Where the content of $pdbs_to_minmize is:
S_0025.pdb S_0948.pdb S_0728.pdb S_0564.pdb S_0484.pdb
Any help will be apprecaited
Dolev
Category:
Post Situation:
The -l option of Rosetta expects a filename of a text file which lists the PDBs to be used, one per line. It shouldn't be used with a list of PDB files on the commandline. (Hence the error - Rosetta is opening the PDB, then treating the ATOM in the file as the name of a PDB it is supposed to open.)
You're right that the -s option should work with a list of PDBs on the commandline. However minimize_with_cst has a bug in that it treats -s like -l. That bug has now been fixed, but it may be a bit before the next weekly release is released.
Until then, print the list of PDBs into a file, and then pass that filename to the -l option.
Dear Friends and Experts,
I am currently in the process of learning to use Rosetta, and I have encountered an issue while following the instructions in the tutorial.
When I execute the command > ROSETTA_BIN/score_jd2.mpi.linuxgccrelease -in:file:s ~/NH/RST/1ire.pdb, it successfully generates a file called score.sc in my current working directory. However, when I attempt to use the -in:file:l option to specify a list of PDB files in a file called pdblist, I encounter an error.
The command I used is > ROSETTA_BIN/score_jd2.mpi.linuxgccrelease -in:file:l ~/NH/RST/pdblist, and the error message I received is: [FILE]: src/core/import_pose/import_pose.cc [LINE]: 361 [START_MESSAGE] [ERROR] UtilityExitException ERROR: Cannot open file "~/NH/RST/1ire.pdb"
In the pdblist file, I have written the paths to the PDB files on each line: ~/NH/RST/1ire.pdb ~/NH/1ire.pdb
Here is some additional information about my computing environment, which may be helpful: [ROSETTA_VERSION]: 2024.09+release.06b3cf8 [COMMIT_DATE]: 2024-03-07T14:59:22.624665 [APPLICATION]: /home/gaoyunfan/rosetta.source.release-371/main/source/bin/score_jd2.mpi.linuxgccrelease [MODE]: Release [EXTRAS]: mpi (OpenMPI 3.1.6) [OS]: GNU/Linux [COMPILER]: GCC version "11.4.0" [STDLIB]: libstdc++ version 20230528 [START_OPTIONS] -in:file:l=/home/gaoyunfan/NH/RST/pdblist
I would greatly appreciate any assistance or advice you can provide to help me resolve this issue. Thank you in advance for your time and expertise.
Dear Friends and Experts,
I am currently in the process of learning to use Rosetta, and I have encountered an issue while following the instructions in the tutorial.
When I execute the command $> $ROSETTA_BIN/score_jd2.mpi.linuxgccrelease -in:file:s ~/NH/RST/1ire.pdb, it successfully generates a file called score.sc in my current working directory. However, when I attempt to use the -in:file:l option to specify a list of PDB files in a file called pdblist, I encounter an error.
The command I used is $> $ROSETTA_BIN/score_jd2.mpi.linuxgccrelease -in:file:l ~/NH/RST/pdblist, and the error message I received is: [FILE]: src/core/import_pose/import_pose.cc [LINE]: 361 [START_MESSAGE] [ERROR] UtilityExitException ERROR: Cannot open file "~/NH/RST/1ire.pdb"
In the pdblist file, I have written the paths to the PDB files on each line: ~/NH/RST/1ire.pdb ~/NH/1ire.pdb
Here is some additional information about my computing environment, which may be helpful: [ROSETTA_VERSION]: 2024.09+release.06b3cf8 [COMMIT_DATE]: 2024-03-07T14:59:22.624665 [APPLICATION]: /home/gaoyunfan/rosetta.source.release-371/main/source/bin/score_jd2.mpi.linuxgccrelease [MODE]: Release [EXTRAS]: mpi (OpenMPI 3.1.6) [OS]: GNU/Linux [COMPILER]: GCC version "11.4.0" [STDLIB]: libstdc++ version 20230528 [START_OPTIONS] -in:file:l=/home/gaoyunfan/NH/RST/pdblist
I would greatly appreciate any assistance or advice you can provide to help me resolve this issue. Thank you in advance for your time and expertise.
The tilde ("~") is expanded by your shell to the home directory, but only when it's on the command line. If you have it in a list file, Rosetta doesn't know how to expand it to your home directory. What you need to do is to manually expand it, substituting the full path. (You can get this by doing something like `echo ~/` on the command line.)