[gmx-users] Simulation of membrane protein

[James Starlight]

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 ?

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>
>
> ==============================**==========
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20111102/0f8f60b1/attachment.html>