[gmx-users] ERROR in Membrane-protein simulation

[Mark Abraham]

Hi,

You didn't finish writing this email, but I'll bet lunch that you didn't
update the top file like the tutorial suggested :-)

Mark

On Mon, 23 May 2016 17:48 BIJENDRA KHADKA <khadkab at mcmaster.ca> wrote:

> Hello Everyone,
> I received an error (shown below) while trying to run "Adding ion" step
> during
> Protein-membrane simulation. Any advice or suggestions will be greatly
> appreciated.
>
> The steps utilized proior to "Adding Ions" are mention below:
>
> > pdb2gmx -f KALP-15_princ.pdb -o KALP-15_processed.gro -ignh -ter -water
> spc
> Topology file updated (as indicated in tutorial)
> > editconf -f dppc128.pdb -o dppc128.gro
>
> > grompp -f minim.mdp -c dppc128.gro -p topol_dppc.top -o em.tpr
>
> > cat KALP-15_processed.gro dppc128_whole.gro > system.gro
>
> > editconf -f system.gro -o system_box.gro -box 6.41840 6.44350 10.59650
>
> > solvate -cp  system_box.gro -cs spc216.gro -o system_box_sol.gro
>
> >
>
> --
>
> *Bijen*
> --
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