[gmx-users] why no. of atoms doesn't match?

[Justin Lemkul]

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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