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shirtsgroup / InterMol

Conversion tool for molecular simulations
MIT License
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Conversion DESMOND--> AMBER #365

Open icamps opened 4 years ago

icamps commented 4 years ago

I would like to know how to make the conversion DESMOND-->AMBER.

From here, it is tell that the conversion will be DESMOND--> GROMACS --> AMBER.

Using the command:

python convert.py --des_in ~/Documents/01_Sim1-ARB/desmond_md_Sim1-ARB-out.cms --amber --odir ~/Documents/AMBERFormat/01_Sim1-ARB/

I am getting the message:

ERROR 2020-08-18 16:17:04 list index out of range
Traceback (most recent call last):
  File "convert.py", line 663, in _save_amber
    top = pmd.load_file(oname + '.top', xyz=oname + '.gro')
  File "/home/icamps/anaconda3/lib/python3.7/site-packages/parmed/formats/registry.py", line 214, in load_file
    return cls(filename, *args, **kwargs)
  File "/home/icamps/anaconda3/lib/python3.7/site-packages/parmed/gromacs/gromacstop.py", line 251, in __init__
    self.read(fname, defines, parametrize)
  File "/home/icamps/anaconda3/lib/python3.7/site-packages/parmed/gromacs/gromacstop.py", line 374, in read
    atoms = [molecule.atoms[int(w)-1] for w in line.split()]
  File "/home/icamps/anaconda3/lib/python3.7/site-packages/parmed/gromacs/gromacstop.py", line 374, in <listcomp>
    atoms = [molecule.atoms[int(w)-1] for w in line.split()]
IndexError: list index out of range
INFO 2020-08-18 16:17:04 Finished!

and two files are created:

desmond_md_Sim1-ARB-out_converted.top
desmond_md_Sim1-ARB-out_converted.gro

What I am doing wrong? I appreciate any help.

mrshirts commented 4 years ago

So, it's converting Desmond into GROMACS correctly, but not from GROMACS into AMBER. So there is probably something wrong with the GROMACS files. It's impossible to tell from here, though. How many atoms are the .cms files?

icamps commented 4 years ago

In the .cms file are 89531 atoms.

icamps commented 3 years ago

Any ideas?

mrshirts commented 3 years ago

Do you have sample files? It's hard to debug with out sample files to run to replicate the error.

On Mon, Aug 31, 2020 at 8:40 AM Ihosvany Camps notifications@github.com wrote:

Any ideas?

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/shirtsgroup/InterMol/issues/365#issuecomment-683821721, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABATPVCGNZORHV37PCCJEPLSDOY7TANCNFSM4QD7EWFQ .

icamps commented 3 years ago

The files are too big (2.4GB) to share here. Please, you can download the DESMOND files from https://bit.ly/3lBOYzY.