[gmx-users] grompp problems

Moore, Jonathan (J) JMoore2 at dow.com
Wed Oct 4 15:23:32 CEST 2006

I get that sort of error when I edit the .mdp file under Windows (mismatch between Windows and unix end-of-line characters).  To avoid this, I try to never edit an mdp file in Windows.  If I forget, it can be fixed by opening the file under unix and deleting all of the Windows end-of-line characters.


Jonathan Moore, Ph.D.
Research and Engineering Sciences - New Products
Core R&D
The Dow Chemical Company
1702 Building, Office 300E
Midland, MI 48674  USA
Phone:  (989) 636-9765 
Fax: (989) 636-4019
E Mail: jmoore2 at dow.com

-----Original Message-----
From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of Ken Rotondi
Sent: Tuesday, October 03, 2006 5:32 PM
To: Discussion list for GROMACS users
Subject: [gmx-users] grompp problems

Hi all,

I'm having troubles with grompp.

Building .gro and .top files from a .pdb file of a 7 residue peptide 
(61 atoms in uaff) results in a system with  5137 atoms in the gro file 
and a .top file with 1 protein (61 atoms) and 1692 solvent (5076 
atoms). When I ran grompp it fatal erred stating that the "number of 
coordinates in the coordinate file (5137 atoms) does not match topology 
(0 atoms).

My .mdp file had the default

cpp  =  /lib/cpp

so I ran the command; 'which cpp', which returned /usr/bin/cpp

I changed the .mdp to

cpp  =  /usr/bin/cpp

and I get the same error.

If I run grompp with the -pp option the processed top file returned is 

Could this have something to do with the

include  =  -I../top

in the preprocessing section of the .mdp file? It would seem to be the 
only thing left.

This is a linux box running Fedora Core 5. No significant modifications 
were made during the install of either the OS or GROMACS.



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