[gmx-users] Re: grompp problem

[Dongsheng Zhang]

Liu Xin,

Try to change the  cpp option to cpp = /lib/cpp  in you mdp file. Hope
it helps.

On Wed, 2005-12-07 at 11:37, gmx-users-request at gromacs.org wrote:

> 
> Message: 1
> Date: Wed, 7 Dec 2005 19:03:21 +0800
> From: liu xin <zgxjlx at gmail.com>
> Subject: [gmx-users] grompp problem !
> To: gmx-users at gromacs.org
> Message-ID:
> 	<c5eecdc0512070303p3df070dw469fcc6ac79ff15b at 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
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-- 
Dongsheng Zhang <dong at pampas.chem.purdue.edu>