AMBER Archive (2008)

Subject: AMBER: RE: Poly(A)-Poly(T) DNA Tutorial Query

From: Ross Walker (
Date: Thu Nov 06 2008 - 12:37:04 CST

Dear Zgong,


Like I said in my previous reply to you, such questions should be posted to
the AMBER mailing list and not to me directly. See to
sign up.


In answer to your problem I suggest that you work through some of the other
tutorials and also do some background reading on molecular dynamics - take a
look at some of the papers as well such as the Cornell et al JACS 94 paper.
This will give you an idea of the concept of atom types and parameters and
you will then better understand what this error message means and why it


Basically it is sayign that atom OP2 does not have a type - this means that
the residue OP2 belongs to does not match the corresponding atom maps. This
is because there is no atom called OP2 in an RC residue - take a look at
$AMBERHOME/dat/leap/prep/ and search for RC. You will see:






   4 P P M 3 2 1 1.60 119.04 200.00 1.1662

   5 O1P O2 E 4 3 2 1.48 109.61 150.00 -0.7760

   6 O2P O2 E 4 3 2 1.48 109.58 20.00 -0.7760



So as you see there is an atom called O2P with atom type O2 but nothing for
OP2 - You should have got an error message when you loaded your pdb file
about this unrecognized atom long before you actually tried to save the
prmtop file.


This problem suggest one of two things - either one the naming in your pdb
file is not kosha and OP2 should be renamed O2P or alternatively there
should be a TER card before this residue since this should be a terminal
RC5/3 rather than RC. In the later case this was explained clearly in the
first section of Tutorial B1 so you should probably carefully re-read this.


Good luck,




From: z g []
Sent: Thursday, November 06, 2008 7:26 AM
To: Ross Walker
Subject: Re: Poly(A)-Poly(T) DNA Tutorial Query


Dear sir:
      when I use amber to do the molecular dynamics of RNA molecules, I have
some problems
I downloaded the PDB file from the PDB database online, However, When I use
the Leap to creat the prmtop and inpcrd files
some errors said "ATOM .R<RC 10> A<OP2 33> does not have a type .....
How can I do about this situation?
Thank you very much!

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