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Hello,
I am working on IDPs. As their are so many advanced force fields developed. I am using that force field for IDP simulation. Now I want to analyze some part of the trajectory with MDAnalysis. But whenever i am giving topology file to read, it shows me error File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 110, in _topology_from_file_like
topology = p.parse(**kwargs)
^^^^^^^^^^^^^^^^^
File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/topology/TOPParser.py", line 226, in parse
raise ValueError(emsg)
ValueError: top_prot_wat.prmtop is detected as a Chamber-style TOP file. At this time MDAnalysis does not support such topologies
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home2/munazzah/Project2/Methods/GaMD/Mix_traj/c_Myb/6.Analysis/KD/test4.py", line 13, in
u = mda.Universe("top_prot_wat.prmtop", "gamd.m.nc")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 356, in init
topology = _topology_from_file_like(self.filename,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 125, in _topology_from_file_like
raise ValueError(
ValueError: Failed to construct topology from file top_prot_wat.prmtop with parser <class 'MDAnalysis.topology.TOPParser.TOPParser'>.
Error: top_prot_wat.prmtop is detected as a Chamber-style TOP file. At this time MDAnalysis does not support such topologies . Is the MDAnalysis module not compatible with this type of topology? Is there some other way to study this type of topology file?
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Hello,
I am working on IDPs. As their are so many advanced force fields developed. I am using that force field for IDP simulation. Now I want to analyze some part of the trajectory with MDAnalysis. But whenever i am giving topology file to read, it shows me error File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 110, in _topology_from_file_like
topology = p.parse(**kwargs)
^^^^^^^^^^^^^^^^^
File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/topology/TOPParser.py", line 226, in parse
raise ValueError(emsg)
ValueError: top_prot_wat.prmtop is detected as a Chamber-style TOP file. At this time MDAnalysis does not support such topologies
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home2/munazzah/Project2/Methods/GaMD/Mix_traj/c_Myb/6.Analysis/KD/test4.py", line 13, in
u = mda.Universe("top_prot_wat.prmtop", "gamd.m.nc")
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 356, in init
topology = _topology_from_file_like(self.filename,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/apps/anaconda3/lib/python3.12/site-packages/MDAnalysis/core/universe.py", line 125, in _topology_from_file_like
raise ValueError(
ValueError: Failed to construct topology from file top_prot_wat.prmtop with parser <class 'MDAnalysis.topology.TOPParser.TOPParser'>.
Error: top_prot_wat.prmtop is detected as a Chamber-style TOP file. At this time MDAnalysis does not support such topologies . Is the MDAnalysis module not compatible with this type of topology? Is there some other way to study this type of topology file?
Thanks
Munazzah Ansari
PhD student
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