Error identifying new atomtypes in $RADII_LIB while adding new residue into modeller topology library
I've been trying to add a new residue's (ligand) topology and parameters into modeller library to model accurately. I am following the steps in modeller's FAQ #8: https://salilab.org/modeller/FAQ.html#8. After adding the topology into a copy of "top_heav.lib", and parameters into a copy of "par.lib", and also into copies of "radii.lib" and "solv.lib", I still get errors.
This is the initial script I used: ------------------ [image: image.png] --------------------
The above script gives error in the 5th command-line as follows: ------------------------------ *ERROR Case-1:* >>> env.libs.parameters.append(file='$(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='$(LIB)/top_heav_edited.lib') read_to_681_> topology.submodel read from topology file: 3 read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 23, in read return self.append(file) File "/usr/lib/python3.10/dist-packages/modeller/topology.py", line 28, in append return _modeller.mod_topology_read(self._modpt, self.__libs.modpt, _modeller.ModellerError: read_to_231E> CHARMM atom type is not recognized (not in RADII_LIB): CG2D1O -------------------------------- This happens inspite of the fact that I have added the radii of new atomtypes into "radii.lib" file itself, and not in the copy "radii_edited.lib", as follows: [image: image.png]
On 3/13/24 3:04 AM, Neeraj Kumar T . via modeller_usage wrote: > I've been trying to add a new residue's (ligand) topology and > parameters into modeller library to model accurately.
In all but the most unusual of cases, it is better to treat a ligand as a rigid body using the '.' residue type in your alignment file. It is also substantially easier to do!
> The above script gives error in the 5th command-line as follows: > ------------------------------ > *ERROR Case-1:* > >>> env.libs.parameters.append(file='$(LIB)/radii_edited.lib') > read_pa_233E> No keyword before contents.
This looks like you are trying to read solv.lib and radii.lib as CHARMM parameter files. That won't work, as these files have very different formats. If you need to edit these, the simplest way to do it is to directly edit the files in the Modeller distribution.
> _modeller.ModellerError: read_to_231E> CHARMM atom type is not > recognized (not in RADII_LIB): CG2D1O
CHARMM atom types can be no longer than four characters. This is mentioned in a few places, but not in the FAQ; I'll add it there.
Ben Webb, Modeller Caretaker
Changing the atomtype nomenclature to 4 characters has worked! Thank you !!!
On Thu, Mar 14, 2024 at 12:34 AM Modeller Caretaker < modeller-care@salilab.org> wrote:
> On 3/13/24 3:04 AM, Neeraj Kumar T . via modeller_usage wrote: > > I've been trying to add a new residue's (ligand) topology and > > parameters into modeller library to model accurately. > > In all but the most unusual of cases, it is better to treat a ligand as > a rigid body using the '.' residue type in your alignment file. It is > also substantially easier to do! > > > 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. > > This looks like you are trying to read solv.lib and radii.lib as CHARMM > parameter files. That won't work, as these files have very different > formats. If you need to edit these, the simplest way to do it is to > directly edit the files in the Modeller distribution. > > > _modeller.ModellerError: read_to_231E> CHARMM atom type is not > > recognized (not in RADII_LIB): CG2D1O > > CHARMM atom types can be no longer than four characters. This is > mentioned in a few places, but not in the FAQ; I'll add it there. > > Ben Webb, Modeller Caretaker > -- > modeller-care@salilab.org https://salilab.org/modeller/ > Modeller mail list: https://salilab.org/mailman/listinfo/modeller_usage >
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Modeller Caretaker -
Neeraj Kumar T .