[gmx-users] Membrane protein insertion/orientation methods

[Yasser Almeida Hernández]

Thanks!

I ran LAMBADA and InflateGRO before to embed my protein in a POPC 
membrane, following the tutorial in 
https://code.google.com/p/inflategro2/wiki/TutorialTolC. It is possible 
that my protein is inserted tilted in the membrane.
When program ask for inflating group I choosed 13 (for POPC) and 1 for 
protein. When I run InflateGRO I got this error:

 > 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

I checked for errors about this and it seems tha the system is blowing up...

Any thoughts?

Yasser

Am 21.08.2015 um 12:00 schrieb 
gromacs.org_gmx-users-request at maillist.sys.kth.se:
> Date: Fri, 21 Aug 2015 10:31:58 +0100
> From: "Catarina A. Carvalheda dos Santos"
> 	<c.a.c.dossantos at dundee.ac.uk>
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Membrane protein insertion/orientation
> 	methods
> Message-ID:
> 	<CAGo0FV_f342OxFcqtGrWn4s72bXHe+PA0E+Kz4-uZgw9moUT6Q at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> Hi there,
>
> Lambada + InflateGRO2 is a good combination.
>
> As for which method is the best one is difficult to say. If you read the
> articles you will have a nice idea of the pros and cons of each method and
> then you can decide by yourself. The only thing I can say is that after
> reading them all I went for the aforementioned combination ;)
>
> Cheers,
> On 21 Aug 2015 10:08, "Tsjerk Wassenaar" <tsjerkw at gmail.com> wrote:
>
>> Hi Yasser,
>>
>> InflateGRO and g_membed do not predict the insertion or orientation, but
>> require the protein to be oriented already. With InflateGRO2, Christian
>> Kandt also brought out LAMBADA which may help aligning a protein with the
>> membrane. memembed is also an orientation predictor. However, I usually
>> just get the protein from the orientations of proteins in membranes (OPM)
>> database at http://opm.phar.umich.edu/
>>
>> Cheers,
>>
>> Tsjerk
>>
>> On Fri, Aug 21, 2015 at 10:16 AM, Yasser Almeida Hern?ndez <
>> yasser.almeida.hernandez at chemie.uni-hamburg.de> wrote:
>>
>>> Hi all,
>>>
>>> Among the methods available, which one is the best/more rigorous/popular
>>> for membrane protein insertion/orientation in model bilayers (InflateGRO,
>>> Memembed, g_membed, etc.)?
>>>
>>> Thanks in advance
>>>
>>> Yasser
>>>
>>> --
>>> Yasser Almeida Hern?ndez
>>> 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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>>
>>
>> --
>> Tsjerk A. Wassenaar, Ph.D.
>> --
>> Gromacs Users mailing list
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> ------------------------------
>

-- 
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