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

Mitchell Stanton-Cook s4026869 at student.uq.edu.au
Mon Nov 10 09:25:06 CET 2008

I have had trouble capping N- and C- terminal residues using the 3.3.X 
series of GROMACS. I even think I started a thread about it. Before you 
digg that thread up you should:

i) work out what you want to do
ii) understand what result you should get
iii) do it and check it !!!

If that fails I suggest you search the list for archives for threads 
discussing capping problems.

For the record I got around the problem using  pdb2gmx from the 3.2 or 
3.1 series of GROMACS.



Mark Abraham wrote:
> 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.
> Mark
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