[gmx-users] POPC Membrane + protein dynamics

Justin A. Lemkul jalemkul at vt.edu
Fri Mar 26 21:20:13 CET 2010

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:


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 :)


> thanks in advance,
> Padhu.
>> 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
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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