After adding the topology into a copy of "top_heav.lib", and parameters into a copy of "par.lib", and also into copies of "radii.lib" and "solv.lib", I still get errors.
This is the initial script I used:
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The above script gives error in the 5th command-line as follows:
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ERROR Case-1:
>>> env.libs.parameters.append(file='$(LIB)/radii_edited.lib')
read_pa_233E> No keyword before contents.
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.10/dist-packages/modeller/parameters.py", line 25, in append
return _modeller.mod_parameters_read(self._modpt, self.__libs.modpt,
_modeller.ModellerError: read_pa_233E> No keyword before contents.
>>>
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Therefore, I deleted command-lines 5&6, and executed the following script.
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And executing the above script gave the following error for the 5th command-line:
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ERROR Case-2:
>>> env.libs.topology.read(file='$(LIB)/top_heav_edited.lib')
read_to_681_> topology.submodel read from topology file: 3
read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 23, in read
return self.append(file)
File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 28, in append
return _modeller.mod_topology_read(self._modpt, self.__libs.modpt,
_modeller.ModellerError: read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O
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This happens inspite of the fact that I have added the radii of new atomtypes into "radii.lib" file itself, and not in the copy "radii_edited.lib", as follows: