Hi all,

I tried to use modeller10.4 to build a homology model for a peptide, which contains a D-Ala. Here the following steps I did:
1: in modlib/top.lib, Copy topology entry of L-Ala, then change

From

IC       N     C     *CA   CB    1.4592    114.4400  123.2300  111.0900  1.5461   

IC       N     C     *CA   HA    1.4592    114.4400  -120.4500 106.3900  1.0840

To

IC       N     C     *CA   CB    1.4592    114.4400  -123.2300 111.0900  1.5461   

IC       N     C     *CA   HA    1.4592    114.4400  120.4500  106.3900  1.0840

Save as DAL

2. In modlib/top_heav.lib, I copied the topology entry for L-Ala and modified it similarly.
3. Added 'DAL' information into modlib/resty.lib.

Despite following these steps, when I ran Modeller10.4, the D-Ala in the peptide appeared identical to L-Ala. Could someone please advise on what might be causing this issue?

Thank you so much.

Wu