Hi all!
I have this protein GFP that I'm working and right now a co-worker of mine
is fixing the parameterization of the chromophore which is the middle of the
protein and so my research professor asked me to run a simulation with the
chromophore cut out of the protein. So I took my pdb file of the GFP molecule
and with the vi editor deleted all the chromophore atoms. I then used
pdb2gmx -f gfp.pdb -ignh
which created my basic topol.top file among other basic files that the command
produces.
I then used the command
editconf -f gfp.pdb -o gfp.pdb -c -d 5 -bt decahedron
which created my box with no problems. I then proceeded to generate water
molecules with this command...
genbox -cp gfp.pdb -o gfpW.pdb -p topol.top -cs spc216.gro
lastly I then used to try to minimize my GFP and thats where things went wrong.
grompp -f em.mdp -c gfpW.pdb -p topol.top -o gfpEM.tpr
The warning I received was
Fatal error:
number of coordinates in coordinate file (gfpW.pdb, 258012)
does not match topology (topol.top, 344648)
I don't get this because I used the pdb file that was used to generate the
topology file and then I continued to tell gromacs to modify the two files
simultaneously after generating water for my box. I am new to gromacs and
finding tutorials that give you all the information you need is near
impossible. I've read the gromacs manual as well and its not very helpful.
Please let me know what I'm doing wrong.
Thanks!
(Gromacian in training) Taylor
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