Re: [AMBER] FATAL: Atom .R<RU5 13>.A<P 29> does not have a type.

From: David A Case <>
Date: Thu, 29 Jan 2015 11:24:21 -0500

On Thu, Jan 29, 2015, Mahad Gatti Iou wrote:

> Loading PDB file: ./chain_B_D.pdb
> Created a new atom named: P within residue: .R<RU5 13>
> Created a new atom named: OP1 within residue: .R<RU5 13>
> Created a new atom named: OP2 within residue: .R<RU5 13> you are getting the expected error involving P, which somehow didn't
show up before.

Your RNA has a 5' phosphate group, which is not in the standard Amber
libraries. The "easy" thing to do is to remove this phosphate if it is
somehow unimportant for your calculation.

To keep the phosphate, you should make a copy of your leaprc file, find
the following line:

     { 0 "U" "U5" } { 1 "U" "U3" }

and remove it. (This is the line that turns the 5' terminal U into a U5
residue). Use this modified leaprc file. I've not sure this is all that
needs to be done, but it should be a good start.


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Received on Thu Jan 29 2015 - 08:30:03 PST
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