[gmx-users] POPC Membrane + protein dynamics
ravi sharma
rdsharma_4u at yahoo.com
Mon Mar 29 12:15:21 CEST 2010
Thanx Justin,
I am somewhat faraway from the topic so can't remember clearly how to define. may be you are right. But this the case where i stuck before.
regards,
Ravi Datta Sharma Lecturer, Bioinformatics,
Department of Microbiology,
CCS Unversity,
Meerut
--- On Sat, 27/3/10, Justin A. Lemkul <jalemkul at vt.edu> wrote:
From: Justin A. Lemkul <jalemkul at vt.edu>
Subject: Re: [gmx-users] POPC Membrane + protein dynamics
To: "Gromacs Users' List" <gmx-users at gromacs.org>
Date: Saturday, 27 March, 2010, 4:59 PM
ravi sharma wrote:
>
> Dear,
> This is the case when you added some ions in your pdb but not define it in your topology, Go in the end of you topology and subtract the number of molecule added. Also define the number of ions added and the name of the ion.
> like :
> NA 14
>
Addition of ions is one possibility, but is not definitively the answer here, especially since the difference in atoms is on the order of 10,000 (roughly 20% of the atoms in the system). In the case of the original post, it is far more likely that there is something more fundamentally wrong with the topology.
Addition of molecules to the topology requires the molecule name, not the atom name, be added to the [molecules] directive. I don't know any force field in Gromacs that uses "NA" as a molecule name; they are all either Na, Na+, or NA+. Any number of molecules subtracted must come from the group in which they are embedded, not just some generic "number of molecules" (stated for the sake of clarity).
-Justin
>
>
> regards,
> Ravi
>
>
>
> --- On *Sat, 27/3/10, Justin A. Lemkul /<jalemkul at vt.edu>/* wrote:
>
>
> From: Justin A. Lemkul <jalemkul at vt.edu>
> Subject: Re: [gmx-users] POPC Membrane + protein dynamics
> To: "Gromacs Users' List" <gmx-users at gromacs.org>
> Date: Saturday, 27 March, 2010, 1:50 AM
>
>
>
> padhu at ncbs.res.in </mc/compose?to=padhu at ncbs.res.in> wrote:
> > hi
> > i have tried as per your justin lemkul's tutorial.
> >
> > after aligning the protein with membrane, subsequently we tried
> to use
> > grompp to generate a tpr file i got the following error.
> >
> > -------------------------------------------------------
> > Program grompp_mpi, VERSION 3.3.1
> > Source code file: grompp.c, line: 448
> >
> > Fatal error:
> > number of coordinates in coordinate file (pope.pdb, 37867)
> > does not match topology (topol_pope.top, 46779)
> > -------------------------------------------------------
> >
> > can any one have idea about how to solve this error.
> >
>
> Please see the general advice:
>
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
> Beyond that, you'll have to post greater details of what step is
> giving rise to this error, what you have done as far as inserting
> the protein, adding solvent and/or ions, etc.
>
> I would also recommend using the latest version of Gromacs (4.0.7),
> unless for some reason you have to use an ancient version (3.3.1). The speed upgrade is incredible :)
>
> -Justin
>
> > thanks in advance,
> > Padhu.
> >
> >>
> >> padhu at ncbs.res.in </mc/compose?to=padhu at ncbs.res.in> wrote:
> >>> Dear All,
> >>> I'm a new comer to gromacs. I need to perform molecular dynamics
> >>> simulation of my protein within the POPC membrane. I have
> downloaded the
> >>> 128a popc lipid from Prof.Tieleman's group along with the required
> >>> popc.itp. My protein of interest is 458 residues. Since the
> 128a popc is
> >>> already Simulated for 1600 ps, i haven't done membrane only
> simulation.
> >>> So
> >>> i directly aligned my protein with the membrane using VMD and
> have saved
> >>> the coordinates. However after i aligned my protein with the
> membrane, i
> >>> felt the membrane was not big enough for my protein of
> interest, also,
> >>> the
> >>> N-terminal region and the loop regions in the C-terminal region and
> >>> stretching outside water molecule above and below
> respectively.ow, i
> >>> have
> >>> two questions here...
> >> Yep, if the protein is sticking "out" of the box on both sides,
> the box is
> >> too
> >> small.
> >>
> >>> 1. How would i increase the number of lipids from the existing one?
> >> Two options:
> >>
> >> 1. genconf -nbox will give integer multiples of the lipid system
> (i.e.,
> >> -nbox 2
> >> 2 1 will expand the bilayer in the x and y directions and give
> 512 lipids)
> >>
> >> 2. genbox -cs popc128a.pdb -box (whatever dimensions) allows you
> a bit
> >> finer
> >> control over how large the box is and how many lipids will result.
> >>
> >>> 2. Also, i should increase increase the number of water
> molecules above
> >>> and below the membrane so that it covers the whole region of
> N-terminal
> >>> and also the loop regions of the C-terminal.
> >> Expand the box using editconf and add solvent with genbox.
> >>
> >>> Now, How to perform these tasks??If i do so will it be
> compatible with
> >>> the
> >>> p
> >
> >
>
> -- ========================================
>
> 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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-- ========================================
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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