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

From: David A Case <>
Date: Fri, 22 Jun 2018 08:40:23 -0400

On Wed, Jun 20, 2018, Kat G wrote:
> 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.

tleap is putting a TER card after DB because there are no bonds between
the DB residue and what follows: the expected O3' -- P bond is not
there. (You can see this by loading your prmtop file into parmed, and
using the printBonds command.)

The missing bond is in turn caused by these lines in your db.lib file:

!entry.DB.unit.connect array int

Atom 35 (which is H22) is the not the atom that should be bonded to the
next residue (i.e. it is not a proper "connect" atom.) It should be 32
instead (which is O3').

If you make that change, you'll get prmtop/inpcrd that look fine, and
the minimized structure doesn't seem to have any problems. If you use
the "savePdb" command in tleap, it is still putting in a TER card: I
don't yet know why. But if you use ambpdb to make the pdb file from the
prmtop and inpcrd files, there is no extra TER card. So you should go
that route if you need a proper PDB file.

...hope this helps...dac

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Received on Fri Jun 22 2018 - 06:00:05 PDT
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