[gmx-users] grompp problems

[Mark Sherman]

A quick way to handle that is the dos2unix utility included in most *nix
systems. It just removes all the dos/windows line delimiters from a
file, but it does it automatically with one step. 

Just for anyone who may need and didn't know about it.


On Wed, 2006-10-04 at 09:23 -0400, Moore, Jonathan (J) wrote:
> 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
> 
> ____________________________
> 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 
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> 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 
> empty
> 
> 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.
> 
> Help,
> 
> Ken
> 
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-- 
______________________________________________
Mark Sherman
Computing Systems Administrator
Informatics Center
Massachusetts Biomedical Initiatives
Worcester, Ma 01605
508-797-4200
msherman at informaticscenter.info
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