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

naresh_sssihl knnaresh at sssihl.edu.in
Wed Sep 18 14:58:31 CEST 2013

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

With Thanks and Best Regards


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