[gmx-users] Membrane protein insertion

[Mark Abraham]

Hi,

Something isn't stable. Check that your membrane protein survives a vacuum
EM (at least). And check your parameter settings for inflategro.

Mark

On Mon, Aug 24, 2015 at 9:53 AM Yasser Almeida Hernández <
yasser.almeida.hernandez at chemie.uni-hamburg.de> wrote:

> 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
> ../1-topology/#4hzuS_popc.top.3#
> Will use a deflating factor of 0.925539817285086 to shrink the lipids
> back in 20 steps
> Deflating
> 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
> Germany
> +49 40 42838 2845
> yasser.almeida.hernandez at chemie.uni-hamburg.de
> office: Grindelallee 117, room 250c
>
> --
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