On 5/2/12 1:09 PM, Sangita Kachhap wrote:
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.
Thanks for reply
When I am appending ligand from .gro file and generating complex the new .gro
file newbox.gro do not have ligand.
Command I have used: editconf -f conf.gro -o newbox.gro -bt dodecahedron -d
1.0
I am appending ligand like this at the end of conf.gro
163ASN HD21 1689 1.029 -0.671 -0.401
163ASN HD22 1690 0.944 -0.584 -0.525
163ASN C 1691 0.621 -0.740 -0.126
163ASN O1 1692 0.624 -0.616 -0.140
163ASN O2 1693 0.683 -0.703 -0.011
1JZ4 C4 1 2.429 -2.412 -0.007
1JZ4 C14 2 2.392 -2.470 -0.139
1JZ4 C13 3 2.246 -2.441 -0.181
1JZ4 C12 4 2.229 -2.519 -0.308
1JZ4 C11 5 2.169 -2.646 -0.295
1JZ4 H11 6 2.135 -2.683 -0.199
1JZ4 C7 7 2.155 -2.721 -0.411
1JZ4 H7 8 2.104 -2.817 -0.407
1JZ4 C8 9 2.207 -2.675 -0.533
1JZ4 H8 10 2.199 -2.738 -0.621
1JZ4 C9 11 2.267 -2.551 -0.545
1JZ4 H9 12 2.306 -2.516 -0.640
1JZ4 C10 13 2.277 -2.473 -0.430
1JZ4 OAB 14 2.341 -2.354 -0.434
1JZ4 HAB 15 2.369 -2.334 -0.528
5.99500 5.19182 9.66100 0.00000 0.00000 -2.99750 0.00000
0.00000
0.00000
Have you correctly incremented the second line of conf.gro to indicate that more
atoms have been added? Without it, editconf will read the wrong number of lines
and exclude the ligand.
-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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