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 > Fax: (989) 636-4019 > E Mail: [EMAIL PROTECTED] > > > -----Original Message----- > From: [EMAIL PROTECTED] [mailto:[EMAIL PROTECTED] 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 > > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] Can't post? Read > http://www.gromacs.org/mailing_lists/users.php > _______________________________________________ > gmx-users mailing list [email protected] > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- ______________________________________________ Mark Sherman Computing Systems Administrator Informatics Center Massachusetts Biomedical Initiatives Worcester, Ma 01605 508-797-4200 [EMAIL PROTECTED] ----------------------~----------------------- _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
