[gmx-users] grompp line too long error

Gianluca Santoni gianluca.santoni at ibs.fr
Thu Nov 24 13:18:43 CET 2011

> Here is the detailed info about my setup:
> System:64-bit Linux
> GMX version:4.5.4
> I know that windows and linux have different line end format and I 
> didn't edit my text files using editor on windows,but all on linux.
Which editor? Problems in principle could arise from your encodings 
setup, even on linux.

> My goal is to simulate membrane protein embeded in lipid bilayer,I 
> don't have experience working with gromacs before,so I followed the 
> tutorial recommended by the official gromacs website:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
> I downloaded the files offered by the tutorial and proceeded and then 
> encountered some problems.
> As there is no lipid molecular defenition in gromacs,the tutorial 
> refered me to this link:
> http://moose.bio.ucalgary.ca/index.php?page=Structures_and_Topologies
> to download the so called "Berger lipids",I did exactly what the 
> tutorial instucted.
> When I called pdb2gmx,I found the nomenclature of atoms in "Berger 
> lipids" is not consistent with that of the gromos53a6 forcefield.
> I abandoned "Berger lipids" because I found the DPPC lipid model 
> offered by Oxford lipidbook is consistent with gromos53a6 
> forcefield,then pdb2gmx worked.You can find the lipidbook here:
> http://lipidbook.bioch.ox.ac.uk/package/show/id/14.html
> After generating the .gro file,I called grompp to generate the .tpr 
> file,and then,grompp throwed the very error message in my original 
> mail.I didn't modify the files generated by the programs I called.
> In order to re-generate the error message, I zipped the forcefield 
> files I used, you can find it here:
> http://ishare.iask.sina.com.cn/f/21401866.html?w='%20target='_blank' 
> <http://ishare.iask.sina.com.cn/f/21401866.html?w=%27%20target=%27_blank%27>

Gianluca Santoni,
Institut de Biologie Structurale
41 rue Horowitz
Please avoid sending me Word or PowerPoint attachments.
See http://www.gnu.org/philosophy/no-word-attachments.html

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