[gmx-users] Simulation of membrane protein

[James Starlight]

Mark,

Firstly I've downloaded Berger's dppc.itp and dppc.gro ( I've already have
had gromos lipid ff)

than I made pdb file for just 1 molecule of the dppc lipid consisted of 50
atoms and generate for that new molecule lipid_posres.itp via pdb2gmx

than I've included lipid_posre.itp to the dppc.itp at the end of file where
the reference for the posres_lipid was already existed as POSRES_LIPID.

I've included in the minim.mdp
define= - DPOSRES_LIPID

than I've minimized my bilayer dppc.gro and checked by VMD if the bilayer
was perturbed after simulation

So althought posres were included in the minim.pdb the bilayer was
perturbed ( tails of lipids were less ordered in comprison to the initial
bilayer )

Why posres didnt work?


2011/11/2 Mark Abraham <mark.abraham at anu.edu.au>

>
>
> On 02/11/11, *James Starlight *<jmsstarlight at gmail.com> wrote:
>
> Justin, Mark,
>
> Ok
> not I've included posre only to the lipid.itp wich consist of parameters
> for just 1 lipid
>
> #ifdef POSRES_LIPID
> #include "posre_lipid.itp"
> #endif
>
> to the minim.mdp I've included
> define        = -DPOSRES_LIPID    ; position restrain the lipids
>
> As the result I have not obtained any error in grompp but after
> minimization my lipid bilayer was perturbed. I've used very strong posres.
> Why it have not worked ?
>
>
> We can't know, because we don't know what's in any files, nor why you
> think the bilayer was perturbed. If you would like useful help, you need to
> be exhaustive in your description of what you have done, what you have
> observed and what you think about those. It is easier for people who might
> volunteer free help to do something else with their time than to ask
> follow-up questions when few details were given originally.
>
> Mark
>
>
>
>
> 2011/10/31 Justin A. Lemkul <jalemkul at vt.edu>
>
>>
>>
>> James Starlight wrote:
>>
>>> I've done all of that
>>> i have "posre_lipid.itp" - for 1 lipid ( posres for each of 50 atoms )
>>>
>>>
>>> I've included this in the topology of the bilayer
>>>
>>> ; Include chain topologies
>>> #include "gromos53a6_lipid.ff/**forcefield.itp"
>>> #include "dppc.itp"
>>>
>>> ; Include water topology
>>> #include "gromos53a6_lipid.ff/spc.itp"
>>>
>>> ; Include ion topologies
>>> #include "gromos53a6_lipid.ff/ions.itp"
>>>
>>> #ifdef POSRES_LIPID
>>> #include "posre_lipid.itp"
>>> #endif
>>>
>>> ; System specifications
>>> [ system ]
>>> 128-Lipid DMPC Bilayer in water
>>>
>>> [ molecules ]
>>> ; molecule name nr.
>>> DPPC 64
>>> SOL              1193
>>> SOL               690
>>>
>>>
>>> Also I've tried to make posre for whole system ( large posres ) but it
>>> also was finished with same error
>>>
>>> Fatal error:
>>> [ file posre_lipid.itp, line 6 ]:
>>> Atom index (2) in position_restraints out of bounds (1-1).
>>> This probably means that you have inserted topology section
>>> "position_restraints"
>>> in a part belonging to a different molecule than you intended to.
>>> In that case move the "position_restraints" section to the right
>>> molecule.
>>> For more information and tips for troubleshooting, please check the
>>> GROMACS
>>> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>>>
>>> What's most true for such multy system. Generate posre only for 1 part
>>> or for whole system?
>>>
>>>
>> Position restraints can only be applied on a [moleculetype] basis.  Thus,
>> order matters a lot, and the whole system cannot be restrained in one file.
>>  See the example here:
>>
>> http://www.gromacs.org/**Documentation/Errors#Atom_**index_n_in_position_
>> **restraints_out_of_bounds<http://www.gromacs.org/Documentation/Errors#Atom_index_n_in_position_restraints_out_of_bounds>
>>
>> As it stands now, the topology you've shown tries to apply lipid position
>> restraints after the ions have been #included, which makes no sense at all.
>>
>>
>> -Justin
>>
>> --
>> ==============================**==========
>>
>> Justin A. Lemkul
>> Ph.D. Candidate
>> ICTAS Doctoral Scholar
>> MILES-IGERT Trainee
>> Department of Biochemistry
>> Virginia Tech
>> Blacksburg, VA
>> jalemkul[at]vt.edu | (540) 231-9080
>> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>>
>> ==============================**==========
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