Hi Xin Liu,

Try using make_ndx (type "make_ndx -h" on your command prompt).
This simple yet useful prog. will then give you an index of all the different
(default) components in your coordinate file. You can then modify groups as you
wish providing you follow the instructions!

I find using make_ndx the easiest way of making sure the topology matches the
coordinates.

I can't understand how it could be to do with the cpp!?

Hope this helps!

Kia 


> Message: 1
> Date: Wed, 7 Dec 2005 19:03:21 +0800
> From: liu xin <zgxjlx@gmail.com>
> Subject: [gmx-users] grompp problem !
> To: gmx-users@gromacs.org
> Message-ID:
> 	<c5eecdc0512070303p3df070dw469fcc6ac79ff15b@mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 
> Dear gmx-users,
> 
> I'm trying to do a minimization of a protein/lipid system, but I get the
> following eroor message when I do grompp:
> 
> merge.top:27:13: warning: no newline at end of file
> ......
> Fatal error: number of coordinates in coordinate file (merge.gro, 22404)
> does not match topology (merge.top, 20495).
> 
> My protein contain 5039 atoms, but in the protein.itp there's just 3130
> atoms, I notice that 22404 - 20495 = 5039 - 3130, it seems that the
> protein.itp misses some atoms. I generate the protein.itp by the following
> steps: pdb2gmx -f -ignh -ter protein.pdb -o protein.gro -p protein.top,
> then choose the "0: Gromacs Forcefield (see manual)", and select "none" when
> asked to "Select C/N-terminus type", finally I rename the protein.top to
> protein.itp and include it into the topology file.
> 
> I serched the mailing list, some one said it probably had something to do
> with the cpp, but I don't know how to adjust it, could anybody so kind tell
> me how to solve this problem? I use SUSE 9.2 and gromacs version 3.1.4.
> 
> Xin Liu

Kia Balali-Mood PhD, CBiol, MIBiol
Postdoctoral Research Associate, Department of Biochemistry, 
Oxford University, OX1 3QU, UK
sansom.biop.ox.ac.uk/kia/ , tel. +44 (0)1865 275 (380 or 275)