[gmx-users] KALP-15 in DPPC tutorial

[RINU KHATTRI]

firstly go back to check your system.gro file which you made bu cat
DPPC.gro new_box.gro >system.gro
remove some line between the merging of two file update the no of atoms
then do your next step


On Mon, Mar 16, 2015 at 9:38 AM, BAOLIN HUANG <baolin.huang at qut.edu.au> wrote:
> Hi All,
> I am doing the GROMACS Tutorial of KALP-15 in DPPC.
> Now, I get stuck at "Note how many lipids were deleted and update the [ molecules ] directive of your topology accordingly. Run energy minimization. Then, scale down the lipids by a factor of 0.95 (assuming you have used default names, the result of the minimization is called "confout.gro"): perl inflategro.pl confout.gro 0.95 DPPC 0 system_shrink1.gro 5 area_shrink1.dat"
>
> The command line was gmx grompp -f minim.mdp -c system_inflated.gro -p topol.top -o em.tpr. And I got Fatal error: number of coordinates in coordinate file (system_inflated.gro, 6438) does not match topology (topol.top 888444) I tried to add DPPC 128 in the [ molecules ], however, I got Fatal error: No such moleculetype DPPC.
>
> How to update the [molecules] in topol.top? And how do I know the number of molecules?
>
>
>
> Kind regards,
>
> Alex Huang
>
>
>
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