Hi,
I’m running the tutorial: Protein MD Setup tutorial using BioExcel Building Blocks (biobb).
At the cell:
Create system topology
Import module
from biobb_gromacs.gromacs.pdb2gmx import pdb2gmx
Create inputs/outputs
output_pdb2gmx_gro = pdbCode+‘_pdb2gmx.gro’
output_pdb2gmx_top_zip = pdbCode+‘_pdb2gmx_top.zip’
Create and launch bb
pdb2gmx(input_pdb_path=fixed_pdb,
output_gro_path=output_pdb2gmx_gro,
output_top_zip_path=output_pdb2gmx_top_zip)
I receive the following:
2023-09-25 12:31:20,113 [MainThread ] [INFO ] Executing biobb_gromacs.gromacs.pdb2gmx Version: 4.1.0
2023-09-25 12:31:20,115 [MainThread ] [INFO ] Copy: 1AKI_fixed.pdb to /home/xxxx/biobb_groamacs_tutorial/dummy/06b4bbf9-bdfc-475f-bc97-708bfe2e9a12
GromacsVersionError Traceback (most recent call last)
Cell In[7], line 10
7 output_pdb2gmx_top_zip = pdbCode+‘_pdb2gmx_top.zip’
9 # Create and launch bb
—> 10 pdb2gmx(input_pdb_path=fixed_pdb,
11 output_gro_path=output_pdb2gmx_gro,
12 output_top_zip_path=output_pdb2gmx_top_zip)
File ~/.local/lib/python3.10/site-packages/biobb_gromacs/gromacs/pdb2gmx.py:172, in pdb2gmx(input_pdb_path, output_gro_path, output_top_zip_path, properties, **kwargs)
165 def pdb2gmx(input_pdb_path: str, output_gro_path: str, output_top_zip_path: str,
166 properties: dict = None, **kwargs) → int:
167 “”“Create :class:Pdb2gmx <gromacs.pdb2gmx.Pdb2gmx> class and
168 execute the :meth:launch() <gromacs.pdb2gmx.Pdb2gmx.launch> method.”“”
170 return Pdb2gmx(input_pdb_path=input_pdb_path, output_gro_path=output_gro_path,
171 output_top_zip_path=output_top_zip_path, properties=properties,
→ 172 **kwargs).launch()
File ~/.local/lib/python3.10/site-packages/biobb_common/tools/file_utils.py:362, in launchlogger..wrapper_log(*args, **kwargs)
354 @functools.wraps(func)
355 def wrapper_log(*args, **kwargs):
356 args[0].out_log, args[0].err_log = get_logs(
357 path=args[0].path,
358 prefix=args[0].prefix,
359 step=args[0].step,
360 can_write_console=args[0].can_write_console_log,
361 )
→ 362 value = func(*args, **kwargs)
363 handlers = args[0].out_log.handlers[
364 :
365 ] # Create a copy [:] of the handler list to be able to modify it while we are iterating
366 for handler in handlers:
File ~/.local/lib/python3.10/site-packages/biobb_gromacs/gromacs/pdb2gmx.py:140, in Pdb2gmx.launch(self)
138 if not self.container_path:
139 if self.gmx_version < 512:
→ 140 raise GromacsVersionError(“Gromacs version should be 5.1.2 or newer %d detected” % self.gmx_version)
141 fu.log(“GROMACS %s %d version detected” % (self.class.name, self.gmx_version), self.out_log)
143 # Run Biobb block
GromacsVersionError: Gromacs version should be 5.1.2 or newer 0 detected
I use Ubuntu 22.04 and from the shell:
$ pip3 list | grep biobb
biobb-analysis 4.1.0
biobb-chemistry 4.1.0
biobb-common 4.1.0
biobb-gromacs 4.1.0
biobb-io 4.1.0
biobb-model 4.1.0
biobb-pmx 4.1.0
biobb-structure-checking 3.13.4
biobb-structure-utils 4.1.0
biobb-vs 4.1.1
pmx-biobb 4.1.3
$ which gmx
/usr/local/gromacs/bin/gmx
$ gmx
GROMACS - gmx, 2023.2 (-:
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/xxxx
Command line:
gmx
SYNOPSIS
gmx [-[no]h] [-[no]quiet] [-[no]version] [-[no]copyright] [-nice ]
[-[no]backup]
OPTIONS
Other options:
-[no]h (no)
Print help and quit
-[no]quiet (no)
Do not print common startup info or quotes
-[no]version (no)
Print extended version information and quit
-[no]copyright (no)
Print copyright information on startup
-nice (19)
Set the nicelevel (default depends on command)
-[no]backup (yes)
Write backups if output files exist
Additional help is available on the following topics:
commands List of available commands
selections Selection syntax and usage
To access the help, use ‘gmx help ’.
For help on a command, use ‘gmx help ’.
Where I’m wrong?
Thanks.
Saverio