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Problem in using prep-tools to prepare the N-terminal res NNNE #3

Closed starwingc closed 4 months ago

starwingc commented 4 months ago

Hi @vvoelz ,

I encounter one issue when I try to build the N-terminal NNNE

the NNNE path is

/peptoid_24summer/residues/GAFF/N_terminal/modified/NNNE/NNE.mol

the command is:

python ~/Voelz_Lab/git/prep-tools/scripts/build_amber_residue.py -t C NNE.mol2 NNNE CappingAtoms.dat N G 0

the error is:

(AmberTools20) starwingchen@90-9c-4a-cf-d5-8d NNNE % python ~/Voelz_Lab/git/prep-tools/scripts/build_amber_residue.py -t C NNE.mol2 NNNE CappingAtoms.dat N G 0
prep-tools, Version 1.0
Environment variable AMBERHOME = /Users/starwingchen/anaconda3/envs/AmberTools20 exists.
Environment variable AMBERHOME = /Users/starwingchen/anaconda3/envs/AmberTools20 exists.
AMBERHOME = /Users/starwingchen/anaconda3/envs/AmberTools20
Building from file NNE.mol2 ...
>> antechamber -i NNE.mol2 -fi mol2 -o NNE.preedit.mol2 -fo mol2 -at gaff -nc 0 -ek "scfconv=1.d-7 tight_p_conv=0" -j 5 -c bcc
Traceback (most recent call last):
  File "/Users/starwingchen/Voelz_Lab/git/prep-tools/scripts/build_amber_residue.py", line 201, in <module>
    out_mol2 = build_antechamber(p.InputFileName, p.ResidueName, CappingAtoms, p.CNTerm, p.Forcefield, p.NetCharge, HeadAtom=p.HeadAtom, TailAtom=p.TailAtom)
  File "/Users/starwingchen/Voelz_Lab/git/prep-tools/scripts/build_amber_residue.py", line 63, in build_antechamber
    run_cmd(command)
  File "/Users/starwingchen/Voelz_Lab/git/prep-tools/scripts/build_amber_residue.py", line 30, in run_cmd
    output = subprocess.check_output(cmd, stderr=subprocess.STDOUT, shell=True)
  File "/Users/starwingchen/anaconda3/envs/AmberTools20/lib/python3.9/subprocess.py", line 424, in check_output
    return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
  File "/Users/starwingchen/anaconda3/envs/AmberTools20/lib/python3.9/subprocess.py", line 528, in run
    raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'antechamber -i NNE.mol2 -fi mol2 -o NNE.preedit.mol2 -fo mol2 -at gaff -nc 0 -ek "scfconv=1.d-7 tight_p_conv=0" -j 5 -c bcc' returned non-zero exit status 1.