[gmx-users] Energy minimisation of solvated protein - Tutorial

[Tsjerk Wassenaar]

Hi Anna,

You should mention the version of Gromacs you're using. One of the
versions did not write the box correctly to pdb files, which I think
happened in your case. If you take as the solvation step

genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.gro

instead of writing output to 1qlz-water.pdb, I think you should be fine.

The reason for writing a .pdb file is the easier visualization with a
multitude of programs.

Thanks for your interest in the tutorial.

Cheers,

Tsjerk

On Fri, Feb 26, 2010 at 1:27 PM, Anna Duncan
<anna.duncan at mrc-mbu.cam.ac.uk> wrote:
> Hi,
>
> I've been trying to go through the 'Introduction to Molecular Dynamics
> Simulations and Analysis' tutorial written by Tsjerk Wassenaar, one of the
> tutorials listed on the GROMACS website.
>
> I've got to the stage where I am performing energy minimisation on my
> solvated protein but when I use grompp to create the .tpr file for mdrun, I
> get the error message:
>
> One of the box lengths is smaller than twice the cut-off length. Increase
> the box size or decrease rlist
>
>
> I am using the protein with pdb ID 1QLZ, one of the suggested structures for
> the tutorial and have so far carried out the following commands:
>
> % pdb2gmx -f 1qlz.pdb -o 1qlz.gro -p 1qlz.top -ignh
> % grompp -f minim.mdp -c 1qlz.gro -p 1qlz.top -o 1qlz-EM-vacuum.tpr
> % mdrun -v -deffnm 1qlz-EM-vacuum.tpr -c 1qlz-EM-vacuum.pdb
> % editconf -f 1qlz-EM-vacuum.pdb -o 1qlz-PBC.gro -bt dodecahedron -d 1.0
> % genbox -cp 1qlz-PBC.gro -cs spc216.gro -p 1qlz.top -o 1qlz-water.pdb
> % grompp -v -f minim.mdp -c 1qlz-water.pdb -p 1qlz.top -o 1qlz-water.tpr
> % genion -s 1qlz-water.tpr -o 1qlz-solvated.pdb -conc 0.15 -neutral -pname
> NA+ -nname CL-
> % grompp -v -f minim_pbc.mdp -c 1qlz-solvated.pdb -p 1qlz.top -o
> 1qlz-EM-solvated.tpr
>
> after which I receive the error message.
>
> The minim_pbd.mdp file I use in the last grompp command is the same as
> minim.mdp used in previous grompp commands (the latter file I downloaded as
> part of the tutorial) except that the line 'pbc = no' has been replaced by
> 'pbc = xyz'.
>
> I have tried increasing the value of 'd' in the editconf command, to 2,3 and
> even 8 but this doesn't make any difference.  (I have read that it is not a
> good idea to tamper with the cut-off values so have avoided doing that)  The
> box vector lengths when d = 1.0 are all 7.10051, and rvdw, rcoulomb = 1.0 in
> mimim.mdp and minim_pbd.mdp, so I don't understand what is going wrong...
>
> Anna
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-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist