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.
Cheers
Mitch
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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