[gmx-users] Regarding errors

Mark Abraham Mark.Abraham at anu.edu.au
Fri Apr 27 08:57:58 CEST 2012

On 27/04/2012 3:53 PM, seera suryanarayana wrote:
> Respected sir,
>                    While i am running the gromacs software i am 
> getting the following error.Kindly tell me how to over come the error.
> Fatal error:
> Atom HA in residue LYS 1 was not found in rtp entry LYSH with 15 atoms
> while sorting atoms.

Please check out 
http://www.gromacs.org/Support/Mailing_Lists#Mailing_List_Etiquette for 
advice on how to construct effective requests for help. With only the 
above information, all that can be said is that the tool you were using 
expected residue LYS that was first in some sequence, and that was being 
mapped to .rtp entry LYSH, to lack atom an atom named HA. Background 
information on the required matching can be found in chapter 5 of the 
manual. Details of how the mismatch occurred can only be found in the 
files you have constructed.


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