[AMBER] creating 5' phosphate groups

From: David A Case <david.case.rutgers.edu>
Date: Mon, 21 Nov 2016 17:36:13 -0500

Aha:: found my earlier post about 5' phosphate groups...didn't make it to
the reflector before....dac

On Mon, Nov 21, 2016, Mohaddeseh Habibzadeh wrote:

> I am trying to prepare the input files for amber simulation on a RNA.

Your RNA (apparently) has a 5' phosphate group at the beginning of a strand.
The standard Amber libraries assume that there is no such group.

To accommondate this, you will need to edit your input pdb file, making one
of the terminal oxygens on the 5' phosphate appear in an OHE residue, rather
than the "G" residue it probably has in your current pdb file.

> When I load my pdb file there is 3 errors:
> FATAL: Atom .R<RG5 1>.A<P 33> does not have a type.

I see that you are using an old version of AmberTools. I think the OHE
suggestion will still work, but would recommend upgrading to AmberTools16.

> AMBER can not identify P, OP1 and OP2 at the beginning of the strand,
> but when i delete them, the unit will be ok!!!

This is correct: if the P, OP1 and OP2 are deleted, you get back to what
Amber's standard libraries expect. But it also looks like you have an
incomplete 5' phosphate group (with only three oxygens attached to the
phosphorus atom.) If this is the case, you will need to build the 4th oxygen
and put it into the OHE residue mentioned above.

Of course, if you don't care about the 5' phosphate, you can delete the P, OP1
and OP2 atoms.


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Received on Mon Nov 21 2016 - 15:00:02 PST
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