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 /<[email protected]>/* wrote:
From: Justin A. Lemkul <[email protected]>
Subject: Re: [gmx-users] POPC Membrane + protein dynamics
To: "Gromacs Users' List" <[email protected]>
Date: Saturday, 27 March, 2010, 1:50 AM
[email protected] </mc/[email protected]> 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.
>
>>
>> [email protected] </mc/[email protected]> 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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