[gmx-users] Simulation of membrane protein

[Kukol, Andreas]

1) Ensure that lipid_posres.itp was included in the topology by using grompp -pp processed.top
2) Check the content of lipid_posres.itp (often the P-atoms are restraint only and not the tails), you may post an extract of that file to the mailing list.

Andreas

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From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org] On Behalf Of James Starlight
Sent: 03 November 2011 10:33
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Simulation of membrane protein

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

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 | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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