Error when generate Martini topology and coordinates

[Clare-xiong]

I use Git Bash on a Windows operating system. When I specify a force field, such as -ff martini303v.partition, I receive an error message:File "D:\program\Anaconda3\Scripts\martinize2", line 558, in entry raise ValueError('Unknown force field "{}".'.format(args.to_ff)) ValueError: Unknown force field "martini303v.partition". When I do not specify a force field and use the default one, I receive this error message: Traceback (most recent call last): File "D:\program\Anaconda3\Scripts\martinize2", line 818, in entry() File "D:\program\Anaconda3\Scripts\martinize2", line 645, in entry AnnotateDSSP(executable=args.dssp, savedir='.').run_system(system) File "D:\program\Anaconda3\lib\site-packages\vermouth\processors\processor.py", line 37, in run_system mols.append(self.run_molecule(molecule)) File "D:\program\Anaconda3\lib\site-packages\vermouth\dssp\dssp.py", line 470, in run_molecule annotate_dssp(molecule, self.executable, self.savedir) File "D:\program\Anaconda3\lib\site-packages\vermouth\dssp\dssp.py", line 301, in annotate_dssp secstructs = run_dssp(system, executable, savefile) File "D:\program\Anaconda3\lib\site-packages\vermouth\dssp\dssp.py", line 197, in run_dssp process = subprocess.run(["dssp", "--version"], stdout=subprocess.PIPE, stderr=subprocess.PIPE) File "D:\program\Anaconda3\lib\subprocess.py", line 505, in run with Popen(*popenargs, **kwargs) as process: File "D:\program\Anaconda3\lib\subprocess.py", line 951, in init self._execute_child(args, executable, preexec_fn, close_fds, File "D:\program\Anaconda3\lib\subprocess.py", line 1420, in _execute_child hp, ht, pid, tid = _winapi.CreateProcess(executable, args, FileNotFoundError: [WinError 2] ϵͳ▒Ҳ▒▒▒ָ▒▒▒▒▒ļ▒▒▒ How can I solve this problem?

[fgrunewald]

can you provide your complete command line?

[Clare-xiong]

My comand line is martinize2 -f 5oqv.pdb -ff martini303v.partition -x CG.pdb -o topol.top -dssp deep -elastic -merge A,B,C,D,E,F,G,H,I

[fgrunewald]

There is no force-field called martini303v.partition in the library and the -dssp program has to be called dssp see bug #506

[Clare-xiong]

I download the Martini 3 open-beta version, and it has a file named martini303v.partition, this force-field was used in the tutorial.

[fgrunewald]

@Clare-xiong the open-beta tutorials are outdated. Please have a look at the more recent tutorials or book chapters on this matter. Unfortunately, we do not have the capacity to guide you step by step on how to utilise Martini protein simulations. Thus I transfer this issue to a discussion.