[gmx-users] Membrane protein insertion
Yasser Almeida Hernández
yasser.almeida.hernandez at chemie.uni-hamburg.de
Tue Aug 25 14:45:45 CEST 2015
Thanks!
My protein is 200 amino acids single chain molecule. I tried the
minimization in vacuo (potential.xvg), using the em.mdp file (see
attached). I feel that the system is not really minimized. I check the
pdb file and it seems ok. Shall I start again with the in vacuum
minimized structure?
What do you think?
Best
Yasser
Am 24.08.2015 um 17:07 schrieb
gromacs.org_gmx-users-request at maillist.sys.kth.se:
> ------------------------------
>
> Message: 2
> Date: Mon, 24 Aug 2015 12:33:08 +0000
> From: "Nash, Anthony" <a.nash at ucl.ac.uk>
> To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> Subject: Re: [gmx-users] Membrane protein insertion
> Message-ID: <D200CD32.56FB%uccaja0 at live.ucl.ac.uk>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi,
>
>
> I used this method recently and I was experiencing the same errors. As
> Mark suggested, makes sure your protein survives an energy minimisation.
> My error was a result of poor preparation of the .pdb file before running
> pdb2gmx. My .itp file contained a long bond between the C and N termini of
> a dimer.
>
> IF you have any doubts, try running InflateGRO2 using a very small part of
> your protein (1 chain) and see if it works.
>
> Anthony
>
> On 24/08/2015 08:59, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>
>> 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 Hern?ndez <
>> 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 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
>>>
>>> --
>>> Gromacs Users mailing list
>>>
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>>> posting!
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>> --
>> Gromacs Users mailing list
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>
> ------------------------------
>
> Message: 3
> Date: Mon, 24 Aug 2015 15:55:40 +0200
> From: Andreas Mecklenfeld <a.mecklenfeld at tu-braunschweig.de>
> To: gmx-users at gromacs.org
> Subject: [gmx-users] Coulomb barriers and Coulomb Softcore Potential
> Message-ID: <55DB225C.8030904 at tu-braunschweig.de>
> Content-Type: text/plain; charset=utf-8; format=flowed
>
> Dear Gromacs-Users,
>
> I want to calculate the solvation free energy of water in an aqueous
> ionic solution and I'm using the Python tool "alchemical-analysis.py" by
> Klimovich, Shirts and Mobley for evaluation. This tool demonstrates a
> very high N/N_k ratio (up to 7000) while decreasing the electrostatic
> potential (Lennard Jones fully active).
>
> Considering energetic barriers, I would like to adjust the Coulomb
> Softcore Potential. Does this seem plausible and if so, how is the
> Coulomb Softcore Potential defined in Gromacs?
> Naden and Shirts provide a concept by equation (A.2) in "Linear Basis
> Function Approach to Efficient Alchemical Free Energy Calculations. 2.
> Inserting and Deleting Particles with Coulombic Interactions"
> (http://pubs.acs.org/doi/abs/10.1021/ct501047e) - is this the formula
> intended?
>
> Best regards,
> Andreas
>
--
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
-------------- next part --------------
; em.mdp - used as input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent minimization)
emtol = 1000.0 ; Stop minimization when the maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 500000 ; Maximum number of (minimization) steps to perform
; Parameters describing how to find the neighbors of each atom and how to calculate the interactions
nstlist = 1 ; Frequency to update the neighbor list and long range forces
cutoff-scheme = Verlet
ns_type = grid ; Method to determine neighbor list (simple, grid)
coulombtype = PME ; Treatment of long range electrostatic interactions
rcoulomb = 1.0 ; Short-range electrostatic cut-off
rvdw = 1.0 ; Short-range Van der Waals cut-off
pbc = xyz ; Periodic Boundary Conditions (yes/no)
-------------- next part --------------
# This file was created Tue Aug 25 13:37:31 2015
# by the following command:
# g_energy -f em.edr -o potential.xvg
#
# g_energy is part of G R O M A C S:
#
# GROwing Monsters And Cloning Shrimps
#
@ title "Gromacs Energies"
@ xaxis label "Time (ps)"
@ yaxis label "(kJ/mol)"
@TYPE xy
@ view 0.15, 0.15, 0.75, 0.85
@ legend on
@ legend box on
@ legend loctype view
@ legend 0.78, 0.8
@ legend length 2
@ s0 legend "Potential"
0.000000 -985.945068
1.000000 -2386.340088
2.000000 -3210.987793
3.000000 -3618.163818
6.000000 -3744.844971
8.000000 -3934.577881
9.000000 -4027.495361
11.000000 -4120.629883
12.000000 -4198.883789
13.000000 -4239.839844
14.000000 -4305.229492
16.000000 -4377.932129
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