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
1. In modlib/top_heav.lib, I copied the topology entry for L-Ala and modified it similarly. 2. 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