[gmx-users] grompp line too long error
20104227043 at suda.edu.cn
Thu Nov 24 12:04:07 CET 2011
Here is the detailed info about my setup:
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.
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:
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