On 5/2/12 8:14 AM, Sangita Kachhap wrote:
Hello all
I have to do MD simulation of ligand bound membrane protein in lipid bilayer.
Thus I am doing tutorialfor Protein - Ligand tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
I have used following command:
pdb2gmx -f 3HTB_clean.pdb -o conf.gro -water spc
editconf -f conf.gro -o newbox.gro -bt dodecahedron -d 1.0
genbox -cp newbox.gro -cs spc216.gro -p topol.top -o solv.gro
grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
I am getting stuck at last command. Its showing following error:
Fatal error:
number of coordinates in coordinate file (solv.gro, 33049)
does not match topology (topol.top, 33064)
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
Did you follow the link? Did you read
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
?
{But when I calculate number of atom in topol.top and solv.gro it is same}
That's not possible.
When I checked above http: I got that such type of error may be due to cpp
variable is not properly set in the .mdp file.
But When I locate ccp in my system and add it to .mdp file.
"
; LINES STARTING WITH ';' ARE COMMENTS
title = Minimization ; Title of run
cpp =/usr/bin/cpp
; Parameters describing what to do, when to stop and what to save
"
Then also it showing same error.
Please help me to solve this problem.
I am using gromacs-4.5.5 and installed with fftw-3.3.1 .
The cpp parameter is ignored for all Gromacs versions as of 4.5.
Your problem is that you don't have a ligand in your coordinate file. Note that
you're off by 15 atoms, which is exactly how many are in the ligand described in
the tutorial. Go back and read the instructions closely, as appending the
ligand to the protein coordinate file is discussed in detail.
-Justin
--
========================================
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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