[gmx-users] number of coordinates in pdb file does not match number of coordinates in topology file

Taylor Kaplan taylor_kaplan at yahoo.com
Thu Nov 18 02:58:24 CET 2010

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.


(Gromacian in training) Taylor

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