[gmx-users] grompp line too long error

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 24 05:55:58 CET 2011

On 24/11/2011 3:45 PM, 杨伟 wrote:
> I was trying to setup a simulation for membrane in DPPC lipid bilayer 
> following this tutorial:
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html 
> I successfully generated the .gro file for the system.But when I tried 
> grompp to generate the .tpr file,I got the error message shown below:
> -------------------------------------------------------
> Program grompp, VERSION 4.5.4
> Source code file: string2.c, line: 105
> Fatal error:
> An input file contains a line longer than 4095 characters, while the 
> buffer passed to fgets2 has size 4095. The line starts with: '20s'
> For more information and tips for troubleshooting, please check the 
> website at http://www.gromacs.org/Documentation/Errors
> -------------------------------------------------------
> I use strace to trace the sys call of grompp,I have found that grompp 
> opened gurgle.dat,and ended up reading gurgle.dat as text file,while 
> gurgle.dat is a binary file,then grompp throwed the fatal error message.
> What could be the cause of this problem?

I would be more suspicious of your input files than anything else. Make 
sure you edit them with a sensible text editor that uses useful line 
endings. Can you use grompp successfully on a simple test case with 
files you haven't edited?


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