[modeller_usage] Error identifying new atomtypes in $RADII_LIB while adding new residue into modeller topology library

["Neeraj Kumar T ." <>]

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]

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: 

------------------

--------------------

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.

-----------------------------

----------------------------------

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: 

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