Re: [AMBER] creating 5' phosphate groups

From: David A Case <>
Date: Sun, 27 Nov 2016 08:44:06 -0500

On Sun, Nov 27, 2016, Mohaddeseh Habibzadeh wrote:

> 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.

You have to make both the atom name and the residue name match between the PDB
file and the library. The atom name of the oxygen in OHE is "OH" not "O5'"

> 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

Also, you would need to put the OHE residue before the the U residue.

*However, you don't want to change the O5' atom! Your PDB file has a
phosphate with only three oxygens attached to it. You need to leave the O5'
oxygen alone, and add an extra (fourth) oxygen, with residue name OHE and atom
name OH.

(I would be curious to know where this PDB file comes from: I've seen this
behavior before, but don't know its origin.)

...good luck....dac

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Received on Sun Nov 27 2016 - 06:00:04 PST
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