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

From: Bill Ross <>
Date: Wed, 20 Jun 2018 19:05:40 -0700

In case you haven't received an answer (my email was down), it looks
like you may not have set your connect1 atom, maybe a 'tail' atom needs
to be set too. That tells leap to look for a connect0 atom in the next


On 6/20/18 11:40 AM, Kat G wrote:
> 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
> Kat
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Received on Wed Jun 20 2018 - 19:30:02 PDT
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