Re: [AMBER] creating 5' phosphate groups

From: Mohaddeseh Habibzadeh <>
Date: Sun, 27 Nov 2016 14:42:22 +0330

As you mentioned before, I upgrade the AmberTools.
And as you can see below I made one of the terminal oxygens on the 5' phosphate appear in an OHE residue:
FATAL: Atom .R<OHE 2>.A<O5' 1> does not have type.
Did I make a mistake? or would you please tell me where's the problem?
ATOM 1 P U A 1
ATOM 2 OP1 U A 1
ATOM 3 OP2 U A 1
ATOM 4 O5' OHE A 1
ATOM 5 C5' U A 1
ATOM 6 C4' U A 1
ATOM 7 O4' U A 1
Thanks and Regards

On Mon, 11/21/2016 05:36 PM, David A Case <> wrote:
> 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.
> ...dac
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Received on Sun Nov 27 2016 - 03:30:04 PST
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