[gmx-users] Simulation of membrane protein

Mark Abraham Mark.Abraham at anu.edu.au
Thu Nov 3 14:39:36 CET 2011


On 3/11/2011 9:32 PM, James Starlight wrote:
> 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.

Your free use of "lipid_posres.itp", "lipid_posre.itp" and 
"posres_lipid" in your sentences above make it seem like you might not 
have been using a file name that matches your #include.

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

There's an extra space in that line. There's a reason people want to see 
actual input and output and contents of files. Stuff filtered through 
your head is stuff that you might have made an extra mistake with.

>
> 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 )

Sounds like Andreas has the right idea.

>
> Why posres didnt work?

Position restraints aren't magic - they're only applied to specific 
atoms. You need to choose which. The genrestr GROMACS tool may be your 
friend here.

Mark


>
>
> 2011/11/2 Mark Abraham <mark.abraham at anu.edu.au 
> <mailto:mark.abraham at anu.edu.au>>
>
>     On 02/11/11, *James Starlight *<jmsstarlight at gmail.com
>     <mailto: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
>>     <mailto: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
>>
>>             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
>>
>>         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 <http://vt.edu/> | (540) 231-9080
>>         http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>>
>>         ========================================
>>         -- 
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>
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