Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST

From: Andre Serobian <>
Date: Thu, 17 Mar 2011 11:51:37 +1100

The H2'1 and H2'2 names were created in the pdb file when I used
ambpdb -aatm to make the pdb file.
I'll edit the pdb file and try again. Thankyou


----- Original Message -----
From: "case" <>
To: "AMBER Mailing List" <>
Sent: Wednesday, March 16, 2011 10:47 PM
Subject: Re: [AMBER] Assertion failed: nat < 5000, file makeDIST_RST

On Wed, Mar 16, 2011, Andre Serobian wrote:
> "Error no map function for H2'1 DT5"

Your PDB file must be using some old atom names. makeDIST_RST uses the
information in the $AMBERHOME/dat/map.DG-AMBER file, so you can look there.
The PDB standard now uses H2' and H2'' as atom names for deoxy sugar
atoms, not H2'1, H2'2. You need to either change your pdb file or the map
file; the former is probably better.


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