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

[Justin Lemkul]

On 9/30/12 1:06 PM, venkatesh s wrote:
> Respected gromacs users
>                                    now iam buliding the simulation system
> for protein + peptide simulation (manually insert the peptide into the
> protein structure file  after the TER )
> following commands i used here
>
> 1. pdb2gmx  -f 2KW8.pdb -o lpvtg.gro -water tip3p -ignh -chainsep ter
>
> in topol.top file i manually made change as a Protein_chain_A 2 (previously
> it is  1)
> [ molecules ]
> ; Compound        #mols
> Protein_chain_A     2
>

This does not sound correct to me.  You have a large protein and a small 
peptide, correct?  These should be different proteins and different 
[moleculetype] entries, correct?  If this is true, you have two distinct 
proteins, not two copies of the same one.

> 2. editconf -f lpvtg.gro -o lpvtg_newbox.gro -c -d 1.0 -bt dodecahedron
>
> 3. genbox -cp lpvtg_newbox.gro -cs spc216.gro -o lpvtg_solv.gro -p topol.top
>
> 4. grompp -f ions.mdp -c lpvtg_solv.gro -p topol.top -o lpvtg_ions.tpr
>
>
> fatal error
> number of coordinates in coordinate file (lpvtg_solv.gro, 24393)
>               does not match topology (topol.top, 26811)
>
> and i read following link
> http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology
>
> manually may want update topol.top file, if yes can you explain?
>

I think you need to revisit step 1.

-Justin

-- 
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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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