I've been trying to add a new residue's (ligand) topology and parameters into modeller library to model accurately. I am following the steps in modeller's FAQ #8: https://salilab.org/modeller/FAQ.html#8. 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: ------------------ [image: image.png] --------------------
The above script gives error in the 5th command-line as follows: ------------------------------ *ERROR Case-1:* >>> env.libs.parameters.append(file='$(LIB)/radii_edited.lib') read_pa_233E> No keyword before contents. Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3.10/dist-packages/modeller/parameters.py", line 25, in append return _modeller.mod_parameters_read(self._modpt, self.__libs.modpt, _modeller.ModellerError: read_pa_233E> No keyword before contents. >>> -------------------------------
Therefore, I deleted command-lines 5&6, and executed the following script. ----------------------------- [image: image.png] ---------------------------------- And executing the above script gave the following error for the 5th command-line: -------------------------------------- *ERROR Case-2:* >>> env.libs.topology.read(file='$(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 -------------------------------- 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: [image: image.png]
