I really cannot figure out how to transfer a topology file from X-PLOR
format to CHARMM format. Can anyone help me out?
Refer to the CHARMM documentation at www.charmm.org, and look at the
topology files within Modeller (e.g. modlib/top_heav.lib). The CHARMM
and X-PLOR formats are very similar, so this shouldn't be very difficult
to do. Note that you will also need to convert the parameter file.
In most cases, however, treating ligands as block residues (rigid
bodies) works well enough in Modeller, in which case no topology or
parameters are required.