[gmx-users] Insertion protein in the membrane via G_membed
James Starlight
jmsstarlight at gmail.com
Wed Jun 20 09:08:54 CEST 2012
Mark,
I've made changes in the input mdp file
integrator = md
energygrps = Protein_ADN
freezegrps = Protein_ADN
freezedim = Y Y Y
energygrp_table
energygrp_excl = Protein_ADN Protein_ADN
here Protein_ADN is the protein_ligand defined in the index.mdp
than I've processed by grompp without problems
but during insertion step by follow command
g_membed -f input.tpr -p topol.top -n index.ndx -xyinit 0.1 -xyend 1.0 -nxy
1000
here I choose Protein_ADN as the group to be inserted and POP as the group
wich are membrane. Eventually I've obtained another strange error
Moleculetype POP is found both in the group to insert and the rest of the
system.
Because we need to exclude all interactions between the atoms in the group
to
insert, the same moleculetype can not be used in both groups. Change the
moleculetype of the molecules POP in the inserted group.
I've checked my index.ndx and didt not find POP group in my first
Protein_ADN group. Why this error should be ?
2012/6/20 Mark Abraham <Mark.Abraham at anu.edu.au>
> 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>
>
>> 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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