[gmx-users] POPC Membrane + protein dynamics

padhu at ncbs.res.in padhu at ncbs.res.in
Fri Mar 26 21:10:02 CET 2010

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.

thanks in advance,

> 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

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