Closed askusay closed 2 years ago
mrshirts
commented
4 years ago If you are converting AMBER to GROMACS, I would suggest using ParmEd directly (https://parmed.github.io/ParmEd/html/index.html), which is more robust than InterMol, and if it has a problem, will probably have better error messages.
If you are working to convert to something else, repost the issue with those errors!
askusay
commented
4 years ago Hi Michael,
I should have clarified that my target is a desmond .cms file and so Intermol is essential for this conversion. As far as parmed goes, there were certainly no issues converting the amber file to the gromacs format.
I have tried to use the converted .top and .gro files to convert to desmond format attached but a similar message was produced:
python $INTERMOL/convert.py --gro_in parmed_conv.top parmed_conv.gro --desmond --oname from_gro
INFO 2020-05-10 10:17:15 Beginning InterMol conversion
INFO 2020-05-10 10:17:15 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
Traceback (most recent call last):
File "/home/ali/Downloads/InterMol/intermol/convert.py", line 811, in <module>
main()
File "/home/ali/Downloads/InterMol/intermol/convert.py", line 223, in main
system, prefix, gro_in, top_in = _load_gromacs(gromacs_files=args['gro_in'])
File "/home/ali/Downloads/InterMol/intermol/convert.py", line 573, in _load_gromacs
system = gmx.load(top_in, gro_in)
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 38, in load
return parser.read()
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 419, in read
self.create_moleculetype(top_moltype, mol_name, mol_count)
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 727, in create_moleculetype
self.create_bond(bond)
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 804, in create_bond
atoms = [int(n) for n in bond[:n_atoms]]
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 804, in <listcomp>
atoms = [int(n) for n in bond[:n_atoms]]
ValueError: invalid literal for int() with base 10: 'cC'This is the output for converting amber into desmond:
python $INTERMOL/convert.py --amb_in parmed_conv.prmtop step5_input.crd --desmond --oname test_desmond
INFO 2020-05-10 13:02:42 Beginning InterMol conversion
INFO 2020-05-10 13:02:42 InterMol is research software. If you make use of InterMol in scientific publications please cite the following reference:
Shirts, M.R., Klein, C., Swails, J.M. et al. J Comput Aided Mol Des (2016). doi:10.1007/s10822-016-9977-1
/home/ali/Documents/REST/github_issu/parmed_conv.prmtop /home/ali/Documents/REST/github_issu/step5_input.crd
Traceback (most recent call last):
File "/home/ali/Downloads/InterMol/intermol/convert.py", line 811, in <module>
main()
File "/home/ali/Downloads/InterMol/intermol/convert.py", line 231, in main
system, prefix, prmtop_in, crd_in, amb_structure = _load_amber(amber_files=args['amb_in'])
File "/home/ali/Downloads/InterMol/intermol/convert.py", line 655, in _load_amber
system = gmx.load(fromamber_top_in, fromamber_gro_in)
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 38, in load
return parser.read()
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 419, in read
self.create_moleculetype(top_moltype, mol_name, mol_count)
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 727, in create_moleculetype
self.create_bond(bond)
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 804, in create_bond
atoms = [int(n) for n in bond[:n_atoms]]
File "/home/ali/anaconda3/envs/ali_conda/lib/python3.7/site-packages/intermol/gromacs/gromacs_parser.py", line 804, in <listcomp>
atoms = [int(n) for n in bond[:n_atoms]]
ValueError: invalid literal for int() with base 10: 'cC'
rajatkrpal
commented
2 years ago I am having the similar issue when trying to convert AMBER topology and coordinates to desmond cms file. It is a membrane topology.
The command I used is :
python /anaconda3/envs/openmm-system-prep/lib/python3.7/site-packages/intermol/convert.py --amb_in bilayer_propanol.prmtop bilayer_propanol.inpcrd --desmond
The error is similar to one posted above
File "/anaconda3/envs/openmm-system-prep/lib/python3.7/site-packages/intermol/convert.py", line 811, in
askusay
commented
2 years ago Hi rajatkrpal, I eventually solved this issue.
For me, it was the result of membrane residue atoms being scattered around the file i.e. not in one block. Say you are using a POPC membrane with cholesterol in it. You need to ensure that all POPC residues are part of one block and that all cholesterol residues are part of one block. Same with ions, waters and ligands that have the same residue name. This issue happens when the prmtop file is converted to the gromacs format which can have issues when residues are scattered since it lists the molecule types as part of topology file.
If your issue stems from the same source, then this should solve it
Hello,
I have consistently run into an issue when trying to convert amber systems into any other format, where in which this error is printed:
The command I have used is:
python $INTERMOL/convert.py --amb_in step5_input.parm7 step5_input.crd --gromacs --oname test_groInfo about the system: Solvated membrane system generated from charmm GUI
Things I have tried without success:
I would appreciate your advice, please find attached files if needed
files.tar.gz