[gmx-users] Membrane protein insertion

Yasser Almeida Hernández yasser.almeida.hernandez at chemie.uni-hamburg.de
Mon Aug 24 09:53:24 CEST 2015

Hi all,

I want to insert a membrane protein into a model bilayer and I've tried 
several methods. The more straightforward seems to be Memembed, which 
gives an orientation to the membrane. On the other hand this method only 
outputs the "membrane" as dummy balls. How to translate this orientation 
to a model bilayer (DOPC, POPC)?

On the other hand I've tried InflateGRO2 for this purpose and I got this 
error (following the tutorial in 
https://code.google.com/p/inflategro2/wiki/TutorialTolC ):

Back Off! I just backed up ../1-topology/4hzuS_popc.top to 
Will use a deflating factor of 0.925539817285086 to shrink the lipids 
back in 20 steps
grompp -f deflate.mdp -c inflated.gro -p ../1-topology/4hzuS_popc.top -n 
inflated.ndx -o tmp.tpr -maxwarn 1
mdrun -s tmp.tpr -v -deffnm tmp_out -c shrink.00.gro
ERROR: Cannot open GRO file "shrink.00.gro": No such file or directory

The end of the log.out file is this:

Fatal error:
Too many LINCS warnings (1184)
If you know what you are doing you can adjust the lincs warning 
threshold in your mdp file or set the environment variable 
GMX_MAXCONSTRWARN to -1, but normally it is better to fix the problem

Any thoughts?

Thanks in advance

Yasser Almeida Hernández
PhD student
Institute of Biochemistry and Molecular Biology
Department of Chemistry
University of Hamburg
Martin-Luther-King-Platz 6
20146 Hamburg
+49 40 42838 2845
yasser.almeida.hernandez at chemie.uni-hamburg.de
office: Grindelallee 117, room 250c

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