[gmx-users] Insertion protein in the membrane via G_membed
Mark Abraham
Mark.Abraham at anu.edu.au
Wed Jun 20 08:50:41 CEST 2012
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 <jmsstarlight at gmail.com
> <mailto: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
> <mailto: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
> <mailto: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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