[gmx-users] grompp line too long error
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:
> 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:
> 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:
> 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:
Institut de Biologie Structurale
41 rue Horowitz
Please avoid sending me Word or PowerPoint attachments.
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