[gmx-users] Error while simulating Protein in SDS/Water

Mark Abraham mark.j.abraham at gmail.com
Wed Sep 18 15:01:58 CEST 2013

Look at the numbers, count the number of atoms you expect in each
moleculetype, and work out what the mismatch is.


On Wed, Sep 18, 2013 at 2:58 PM, naresh_sssihl <knnaresh at sssihl.edu.in> wrote:
> Dear GMX users,
> I am trying to simulate a protein in SDS/Water box.
> 1. No problems with pdb2gmx - .gro file and .top files were generated.
>     /pdb2gmx -f protein.pdb -o protein_pro.gro -water spce/
> selected ff 13: GROMOS96 53a6 force field (JCC 2004 vol 25 pag 1656)
> 2. Created a Cubic box using editconf
>   /editconf -f protein_pro.gro -o protein_newbox.gro -c -d 1.0 -bt cubic/
> 3. Then solvated the system using genbox
>       genbox -cp protein_newbox.gro -cs spc216.gro -ci sds.gro -nmol 215 -o
> protein_solv.gro -p topol.top
> 4. After this step I looked at the topol.top file and I found that it was
> not fully updated and so I manually updated by adding no. of SDS molecules
> under [ molecules ] section at the very end. Also I added #include sds.itp
> whereever it was required.
> In fact I followed the discussion between Justin, Mark and Anna Marabotti at
> the following link:
> http://lists.gromacs.org/pipermail/gmx-users/2009-June/042704.html  and did
> everything that was suggested.
> 5. When I use grompp after the step 4
>     grompp -f minim.mdp -c protein_solv.gro -p topol.top -o protein.tpr
> This is where I am getting a Fatal Error saying that the number of
> Co-ordinates in protein_solv.gro do not match with the number of
> co-ordinates in topol.top.
> Could you please help regarding this... Please give me your valuable
> suggestions.
> With Thanks and Best Regards
> Naresh
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