On 20/06/2012 4:39 PM, James Starlight wrote:
by the way I've forced with problems during insertion of the complex
protein_ligand into membrane by means of g_membed
firstly I've created index.ndx file with the merged protein_ligand
group. Than I've used next mdp for my g_membed input
integrator = md
energygrps = Protein ADN
freezegrps = Protein ADN
freezedim = Y Y Y
energygrp_table
energygrp_excl = Protein Protein
here ADN is the ligand
than I've tried to generate input file for g_membed where I've
selected my protein_ligand group to be inserted into membrane but I've
obtained this eror althought protein_ligand group were presented in
the list of aviable groups for insertion
Fatal error:
Group Protein_ADN not found in indexfile.
Maybe you have non-default groups in your mdp file, while not using
the '-n' option of grompp.
In that case use the '-n' option.
So clearly you haven't given grompp an index file with the merged
protein-and-ligand group that matches the .mdp file usage. Since you're
changing nomenclature at least once in the course of this email, that's
not surprising. You may not have the patience to check your spelling in
email, but grompp will insist on everything to its satisfaction...
Mark
Finally If I've tried to insert kust protein intoi membrane than
G_membed delete my ligand during insertion
Will remove 0 Protein molecules
Will remove 1 ADN molecules
Will remove 10 POP molecules
Will remove 41 SOL molecules
How I could fix this problem and obtain whole protein_ligand system
inserted in the membrane ?
James
2012/6/15 James Starlight <jmsstarli...@gmail.com
<mailto:jmsstarli...@gmail.com>>
I've found main reason of such crushes. It was due to the
individual internal waters wich I've included to my model as the
buried to the protein interiour ( the coordinates were copppied
form X-ray structure of the same protein).
By the way I have already performed the same simulation with the
inclussion of the same X-ray waters but in different system with
membrane-mimicking env. consisted of Ccl4 in water. As the result
there have not been any problems with that system.
Finally I have some question about G_membed acceleration. I've
noticed that the process of insertion of the protein in the
membrane is very long (actually it's only 50ps simulation).
During procesing of my system I've obtained notes like
NOTE 4 [file topol.top, line 19511]:
For energy conservation with LINCS, lincs_iter should be 2 or
larger.
NOTE 1 [file gmembed.mdp]:
You are using a cut-off for VdW interactions with NVE, for good
energy
conservation use vdwtype = Shift (possibly with DispCorr)
NOTE 2 [file gmembed.mdp]:
You are using a cut-off for electrostatics with NVE, for good energy
conservation use coulombtype = PME-Switch or Reaction-Field-zero
The parameters for long-range and short-range interactions I've
used from my typical simulation on the lipid Gromos56-ff (
presented in the Justin's tutorial).
Is there any other parameters for that object wich are most
suitable for G_membed ?
James
2012/6/14 James Starlight <jmsstarli...@gmail.com
<mailto:jmsstarli...@gmail.com>>
Mark,
I've used commands provided in the G_membed manual
g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0
-nxy 1000
or
g membed -f input.tpr -p merged.top -xyinit 0.1 -xyend 1.0
-nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
In both cases I've obtained the same message
There are 122 lipids in the membrane part that overlaps the
protein.
The area per lipid is 0.5002 nm^2.
Maximum number of lipids that will be removed is 45.
and eventually only 10 lipids were removed. Also I've tried to
do this on another pope bilayer (consisted of bigger lipids
with properly equilirated ) but I've obtained exactly the same
results.
James
2012/6/14 Mark Abraham <mark.abra...@anu.edu.au
<mailto:mark.abra...@anu.edu.au>>
On 14/06/2012 4:39 PM, James Starlight wrote:
Dear Gromacs Users!
I've forced with the problem durin insertion of my
protein into pre-equilibrated bilayer via G_Membed.
I've done all steps in accordance to the KALP tutorial (
I've oriented both membrane as well as the protein in the
same dimensions merged both topologies and gro files in
the merged.gro file ) but after processed via grompp I've
recieved warning
WARNING 1 [file gmembed.mdp]:
Can not exclude the lattice Coulomb energy between
energy groups
You've asked about this before...
http://lists.gromacs.org/pipermail/gmx-users/2011-November/066002.html
if I scip this message by maxwarn oprtins, g_membed
remove only 10 lipids ( while > 40 are overlapped with
the protein ) and during further g_membed's md_run I've
obtained lincs warning and my system is crushed .
Have you followed g_membed -h and their published method?
You've not shown your command lines, so it's impossible
for anyone to know what you're doing.
Mark
I'm using berger lipids and that mdp file for the G_membed
integrator = md
energygrps = Protein
freezegrps = Protein
freezedim = Y Y Y
energygrp_table
energygrp_excl = Protein Protein
emtol = 1000.0 ; Stop minimization when the
maximum force < 1000.0 kJ/mol/nm
emstep = 0.01 ; Energy step size
nsteps = 50000 ; Maximum number of
(minimization) steps to perform
; Bond parameters
constraint_algorithm = lincs ; holonomic constraints
constraints = all-bonds ; all bonds (even heavy atom-H
bonds) constrained
lincs_iter = 1 ; accuracy of LINCS
lincs_order = 4 ; also related to accuracy
; Neighborsearching
ns_type = grid ; search neighboring grid cels
nstlist = 5 ; 10 fs
rlist = 1.2 ; short-range neighborlist
cutoff (in nm)
rcoulomb = 1.2 ; short-range electrostatic
cutoff (in nm)
rvdw = 1.2 ; short-range van der Waals
cutoff (in nm)
; Electrostatics
coulombtype = PME ; Particle Mesh Ewald for
long-range electrostatics
pme_order = 4 ; cubic interpolation
fourierspacing = 0.16 ; grid spacing for FFT
pbc = xyz ; 3-D PBC
Could you tell me where is the problem in my case might be?
James
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