No output file

[zhongweishen]

Hello, I am typing "Python auto_martini -- SDF p4. SDF --mol dox --verbose --fpred" command with an error in the picture and no verbose output.Also, I tried to coarely granulated adriamycin hydrochloride (weight of atoms 37), how to properly disassemble the molecule, I directly changed the PDB file to divide the molecule into four parts, will this affect the electrical properties of each part and thus affect the classification of beads?Here is my doxorubicin hydrochloride and a four-part file.

dox.zip

Could you please give me some guidance? thank you!

[tbereau]

Hi zhongweishen,

Regarding the error message at the end of your output, it might be that you're missing the lxml package. You can install it using pip

pip install lxml

Does this resolve the error message?

As a side note, I would recommend using a SMILES string rather than an SDF file as input (we've done more tests with SMILES).

Best,
Tristan

[zhongweishen]

Thank you very much for your patient reply and please forgive my poor English expression.Now it can run normally, and I use SMILES according to your suggestion.
But I still have some problems,I python in
python auto_martini --smi "OCC(=O)[C@@]1(O)CC@Hc2c(C1)c(O)c1c(c2O)C(=O)c2c(C1=O)cccc2OC" --mol GUA --gro gua.gro
get：usage: auto_martini [-h] (--sdf SDF | --smi SMI) --mol MOLNAME [--aa AA]
[--cg CG] [-v] [--fpred]
auto_martini: error: unrecognized arguments: --gro gua.gro
I can't get the gro file.
I delete "--gro Gua. Gro" for the input instruction, and half way through the calculation I get "killed" and break the process
My molecule contains 39 heavy atoms. Do I need to break it into smaller pieces?

[tbereau]

--gro is a flag that's become obsolete. Instead you should use the optional flags

• --aa for the atomistic coordinates file
• --cg for the coarse-grained coordinates file
  Meaning: try replacing --gro by --cg.

[zhongweishen]

Thank you for your suggestion. It is working normally now

[Kuchenbecker]

Hello @tbereau ! Thanks for you program. I'm trying to use it but still got problems related to No Output File.
I've Installed Anaconda 2, created a env with Python 2.7.X (its 2.7.16 now) and installed all the modules asked in the README file at auto_martini_master.

With all installed i tried to run the program with the GUA example but after run it, it ends at nothing: no output file and no message. If i use --verbose i can see all the INFO:main lines showing the computer working but.... no result at the end.

How can i solv it?

Appreciate the help!

[tbereau]

Hi,

I suppose it's a problem with one of the libraries. Try the following:

#17 (comment)

Do you get any output?

[Kuchenbecker]

Hello,

I did just like asked, running the code i got the output, just as in the imagem bellow.

Any other ideas? I'm trying to figure out but no really working.

[Kuchenbecker]

Somehow i've managed to make it work. I really appreciate all the help. Now, it's working.