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
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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: 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
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 |