[gmx-users] Error while running grompp for em (MD) in Urea

[Mark Abraham]

Anil Kumar wrote:
> Dear All,
> 
> Can anyone help me in running simulation in explicit urea.
> When i was using urea+h2o.gro and urea.itp and tried to do simulation in
> explicit urea.
> After doing genbox, i am not able to do the grompp for energy minimization
> and getting the error which is given below.
> 
> I have added masses of all the atoms of urea in atommass.dat file, but
> still getting the same error.

This file isn't used for making topologies.

> Please help me, where does am i making the mistakes.
> 
> processing coordinates...
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
> Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
> Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)

Well, if these don't match you're doing something wrongly, but I can't 
tell what.

> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> #      BONDS:   945
> #   G96BONDS:   128
> #     ANGLES:   1215
> #  G96ANGLES:   190
> #      PDIHS:   1134
> #      IDIHS:   485
> #       LJ14:   1242
> #     SETTLE:   2050
> ERROR 4 [file "base.top", line 808]:
>   atom C1 (Res UREA-11) has mass 0
> 
> ERROR 5 [file "base.top", line 808]:
>   atom O2 (Res UREA-11) has mass 0
> 
> ERROR 6 [file "base.top", line 808]:
>   atom N3 (Res UREA-11) has mass 0
> 
> ERROR 7 [file "base.top", line 808]:
>   atom H4 (Res UREA-11) has mass 0
> 
> ERROR 8 [file "base.top", line 808]:
>   atom H5 (Res UREA-11) has mass 0
> 
> ERROR 9 [file "base.top", line 808]:
>   atom N6 (Res UREA-11) has mass 0
> 
> ERROR 10 [file "base.top", line 808]:
>   atom H7 (Res UREA-11) has mass 0

Your force field's .rtp file needs entries for these atoms, probably.

Mark