[AMBER] why tleap adds TER in the middle of a DNA sequence

From: Kat G <katwin86.gmail.com>
Date: Wed, 20 Jun 2018 13:40:52 -0500

Dear all,

I have a DNA sequence GG-m6A-CT (5mer.pdb). Based on the parameter of
6MA (N6-Methyladenosine)
from all_modrna08.lib, I modified to get the parameters for my m6A- DNA
version and named it as DB (db.lib attached as db.lib.dat).

I don't know why tleap puts the TER tag after my DB
(DG5-DG-DB-TER-DC-DT3) (5mer-tleap.pdb),
causing the break in the middle of 5-mer during minimization step
(5mer-min.pdb). I am not sure if there is something wrong on the way
obtaining parameters of m6A DNA from RNA type.

Could you please help me to have a look at those attached files.

Thank you so much

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Received on Wed Jun 20 2018 - 12:00:02 PDT
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