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
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