[gmx-users] Insertion protein in the membrane via G_membed
James Starlight
jmsstarlight at gmail.com
Wed Jun 20 08:39:42 CEST 2012
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.
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 <jmsstarlight at 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 <jmsstarlight at 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.Abraham at 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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>>
>>
>
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