[gmx-users] missing of methyl at N-terminal

Mark Abraham Mark.Abraham at anu.edu.au
Mon Nov 10 08:49:28 CET 2008

Bhawana Gupta wrote:
> hello,
> thankyou for ur advice on the mail named *missing of methyl at N-terminal.

Terminology is important to get right. You were capping the *C-terminal* 
end with an *N-methyl*.

> *  i m using forcefield ffgmx.

That's a poor idea for anything other than a learning exercise. That 
force field has been deprecated for years.

> u had advice me to put the correct name 
> for terminal N-CH3 group
> i.e. i had replaced NHM with NAC as given there. That error has been 
> solved but again i m getting the  error as:
> ---------------------------------------------------------
> Program pdb2gmx, VERSION 4.0
> Source code file: pdb2top.c, line: 574
> Fatal error:
> atom N not found in residue 1ACE while combining tdb and rtp
> -----------------------------------------------------
> This is my pdb file in text editor

So what were your pdb2gmx command line and responses to prompts? You 
need to think carefully about why pdb2gmx might be looking for an N atom 
in your ACE residue that doesn't have one.


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