[gmx-users] Errors during energy minimization of POPC membrane

[Roshan Shrestha]

Thanks Justin, but I am not sure how can that be since I downloaded
the force field from Mackerell Lab, did not show any errors while
using it for equilibrating my peptide. How can it show errors for my
bilayer though?

On 10/7/16, Roshan Shrestha <roshanpra at gmail.com> wrote:
> I created a POPC membrane using CHARMM membrane builder, added some water
> into it using gromacs, did not add any ions since it was already neutral,
> then I ran its energy minimization using minim.mdp of lysozyme tutorial.
> However, I ended up with lots of errors like these below after using
> grompp:
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
>
> *ERROR 9779 [file topol.top, line 161668]:  No default U-B typesERROR 9780
> [file topol.top, line 161669]:  No default U-B typesERROR 9781 [file
> topol.top, line 161671]:  No default U-B typesERROR 9782 [file topol.top,
> line 161672]:  No default U-B typesERROR 9783 [file topol.top, line
> 161674]:  No default U-B typesERROR 9784 [file topol.top, line 161675]:  No
> default U-B typesERROR 9785 [file topol.top, line 161677]:  No default U-B
> typesERROR 9786 [file topol.top, line 161678]:  No default U-B typesERROR
> 9787 [file topol.top, line 161680]:  No default U-B typesERROR 9788 [file
> topol.top, line 161681]:  No default U-B typesExcluding 3 bonded neighbours
> molecule type 'Other'Excluding 2 bonded neighbours molecule type
> 'SOL'Removing all charge groups because cutoff-scheme=VerletThere was 1
> note-------------------------------------------------------Program gmx
> grompp, VERSION 5.1.3Source code file:
> /home/roshan/Downloads/gromacs-5.1.3/src/gromacs/gmxpreprocess/grompp.c,
> line: 1738Fatal error:There were 9788 errors in input file(s)*
>
> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
>


-- 
Roshan Shrestha
Graduate Student
Central Department of Physics,Tribhuvan University
Kathmandu,Nepal