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

Justin A. Lemkul jalemkul at vt.edu
Thu Nov 18 03:10:57 CET 2010

Taylor Kaplan wrote:
> 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

Are you filling in the resulting gap with a reasonable "filler" residue?  If 
not, I guarantee your simulation will collapse instantly.

> 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

A box-solute distance of 5 nm is overkill for most common applications.  I 
suspect this is related to your problem (see below).  If nothing else, you're 
certainly going to take a major performance hit simulating a few hundred 
thousand water molecules, most of which are completely unnecessary.

> 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.

Commentary on what would make tutorials more user-friendly would be welcome, 
especially for those of us who work hard to write useful ones.  Just saying 
they're insufficient isn't going to make them any better ;)

I suspect there's a problem with the atom numbering that is allowed by the .pdb 
file.  Due to the huge number of atoms you've got, something might be breaking 
down, but this is a bit of a guess.  In principle, Gromacs should be able to 
deal with any number of atoms, but perhaps something is going wrong.  Try to 
re-build the system (back at the editconf step) with something like -d 1 to 
generate a substantially smaller box and a more suitable number of waters.

The one thing you can certainly check is whether or not the .pdb and .top should 
indeed match.  If you do:

grep -c OW gfpW.pdb

...it should match the number of SOL indicated in topol.top.  If it does, then 
you've probably run into some bizarre problem.  If it doesn't, then something 
else has gone wrong, though from the commands you've provided everything seems 
like it should work.


> Thanks!
> (Gromacian in training) Taylor


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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