On 4/15/13 1:30 PM, Albert wrote:
Hello:
I've build a protein/membrane system with CHARMM-GUI, and I am going to use it
for Gromacs MD simulation with Slipids FF.
First I extract the protein and generate toplogy file by command:
pdb2gmx -f protein.pdb -o gmx.pdb -ignh -ter
The protein was assigned with Amber FF including TIP3P for solvent
after that, I add the following at the top of topol.top file:
; Include forcefield parameters
#include "slipids.ff/forcefield.itp"
#include "ligand.itp"
#include "popc.itp"
#include "chol.itp"
and the following at the bottom of topol.top file:
[ molecules ]
; Compound #mols
Protein_chain_A 1
LIG 1
CHL1 42
POPC 98
SOL 10079
A the new protein coordinate gmx.pdb was replaced CHEARMM-GUI protein
coordinate, all cheloest are put together, all popc were also put together. The
order in the complex.pdb are: protein, ligand, cholestrol, popc and water. The
system contains 1 protein, 1 ligand, 42 chelostrol, 98 POPC and 10079 water
molecules. Then I am trying to minimize the system with command:
grompp_mpi -f em.mdp -c complex.pdb -o em.tpr
However, it always failed with messages:
Program grompp_mpi, VERSION 4.6.1
Source code file: /home/albert/Desktop/gromacs-4.6.1/src/kernel/grompp.c, line:
563
Fatal error:
number of coordinates in coordinate file (complex.pdb, 49531)
does not match topology (topol.top, 51295)
I don't understand why Gromacs claim such kind of errors, since to me,
everything is all right for my pdb file and toplogy...
I'll put my money on grompp being right ;)
Seriously though, the answer to this question is always the same. You're not
counting something right. The solution is something only you can determine.
Applying grep -c is your friend here. You're off by 1764 atoms, which may be
useful information if any of your molecules are evenly divisible into 1764.
Water is, but perhaps other molecules are, as well, depending on their
representation.
-Justin
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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