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
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