pa...@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.
pa...@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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