[gmx-users] Atom N not found....

Justin A. Lemkul jalemkul at vt.edu
Thu Apr 5 12:43:11 CEST 2012

rama david wrote:
> Hi Gromacs friends,
> When I given the command ...
> pdb2gmx -f .. -o .. -p .. -ignh
> I gate the following error..
> ------------------------------------------------------
> Program pdb2gmx, VERSION 4.5.4
> Source code file: /build/buildd/gromacs-4.5.4/src/kernel/pdb2top.c, 
> line: 1070
> Fatal error:
> atom N not found in buiding block 1ACE while combining tdb and rtp
> For more information and tips for troubleshooting, please check the GROMACS
> website at http://www.gromacs.org/Documentation/Errors
> When I goes through the detail of the website at 
> http://www.gromacs.org/Documentation/Errors and document
> I come to know that I have to modify the rtp file,

Nowhere in the explanation of the error does it suggest that you should alter 
the .rtp file in this instance.  You have atoms in your structure that are not 
in the .rtp entry.  Specifically, your structure file has an N atom in ACE, but 
ACE only contains CA, C, and O.  The N atom should be the first atom in the next 
residue, not ACE.



Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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