[gmx-users] NME not found in rtp

Dialing Pretty hdc123hdc123 at yahoo.com
Fri Feb 17 13:54:23 CET 2012

Hi Mark,

It seems you do not work in a molecular dynamics simulation lab, but you are very interested in molecular dynamics simulation, including having answered one of my questions before. Can you explain the reason to me?


 From: Mark Abraham <Mark.Abraham at anu.edu.au>
To: Discussion list for GROMACS users <gmx-users at gromacs.org> 
Sent: Friday, 17 February 2012 10:44 PM
Subject: Re: [gmx-users] NME not found in rtp
On 17/02/2012 10:27 PM, francesca vitalini wrote:
> Hi all!
> I encounter this error while running pdb2gmx on GROMACS3.3.1 with
> ffG53a6m il forcefield modificato per la reverse transformation.
> Fatal error:
> Residue 'NME' not found in residue topology database
> I know I should add it to the .rtp file, but I don't know exactly how
> to do that, any help?

Check the .rtp in case it has this residue under a different name (often 
NAC). Otherwise, you need to check out the relevant part of chapter 5 of 
the manual, and proceed by analogy from the other C-terminal capping 
residues that are there.


> Otherwise, I'm actually just looking for a toy system with which just
> play around as I'm having issues with the reverse transformation. Any
> suggestion for a pdb? thanks!

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