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-requ...@maillist.sys.kth.se:
------------------------------
Message: 2
Date: Mon, 24 Aug 2015 12:33:08 +0000
From: "Nash, Anthony" <a.n...@ucl.ac.uk>
To: "gmx-us...@gromacs.org" <gmx-us...@gromacs.org>
Subject: Re: [gmx-users] Membrane protein insertion
Message-ID: <d200cd32.56fb%ucca...@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.abra...@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.hernan...@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.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c
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------------------------------
Message: 3
Date: Mon, 24 Aug 2015 15:55:40 +0200
From: Andreas Mecklenfeld <a.mecklenf...@tu-braunschweig.de>
To: gmx-us...@gromacs.org
Subject: [gmx-users] Coulomb barriers and Coulomb Softcore Potential
Message-ID: <55db225c.8030...@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.hernan...@chemie.uni-hamburg.de
office: Grindelallee 117, room 250c
; 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)
# 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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