On 10/20/24 11:32 PM, Xiaosa Wu via modeller_usage wrote: > I tried to use modeller10.4 to build a homology model for a peptide, > which contains a D-Ala.

I would do this in one of two ways: either build a model containing ALA, then mutate ALA to DALA and relax; or, if the template contains a DALA, use the '.' residue type to copy it directly into the target.

If you want to model DALA flexibly, modifying the IC entries in top_heav.lib is probably not sufficient. These simply provide the internal coordinates needed to build a structure from scratch. To model a structure, you also need a forcefield, so you may also need to modify the BOND or IMPR lines and/or the corresponding parameters in par.lib. I see that Modeller's default parameters have an improper defined in top_heav.lib for ALA for CA-N-C-CB, with corresponding CT1-NH1-C-CT3 IMPROPER parameters in par.lib, so that would probably need to be adjusted for DALA, perhaps by defining a new atom type for the chiral CA. Something similar is done in CHARMM's parameter files for D-amino acids, albeit for the CMAP correction; see toppar/stream/prot/toppar_all36_prot_c36m_d_aminoacids.str in toppar_c36_jul24.tgz available from http://mackerell.umaryland.edu/charmm_ff.shtml. But I think this would be a lot of work for probably little gain.

Ben Webb, Modeller Caretaker