No such moleculetype UREA

User discussions
1

GROMACS version: 5.1.5
GROMACS modification: No
Here post your question : How to fix the error of no such moleculetype UREA.

Hi everyone,
I am trying to set up a system of GB1 protein in a solvent box containing urea and water and for this I followed the mixed solvent manual of GROMACS. I have completed upto the adding urea and water molecules part successfully but when I am running the adding ions part of the simulation after modifying the topology file by adding the urea.itp file and the molecules directive, the following error pops up:

Fatal error:
No such moleculetype UREA

The modifications in the topology file:

; Include water topology
#include “amber99sb-ildn.ff/spce.itp”

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcx fcy fcz
1 1 1000 1000 1000
#endif

; Include topology for ions
#include “amber99sb-ildn.ff/ions.itp”

:Include topology for urea
#include “amber99sb-ildn.ff/urea.itp”

[ system ]
; Name
IMMUNOGLOBULIN G-BINDING PROTEIN G in water

[ molecules ]
; Compound #mols
Protein_chain_A 1
Protein_chain_B 1
UREA 825
SOL 8746

In the gro file the molecule name for urea is also written as UREA.

Please help me how to fix this error.

Thanks and regards,

Sweta.

2

Hi,
In directive [molecules] UREA is before SOL
You can include urea.itp before spce.itp in the topology.
Kind regards
Alessandra

3

OK, thanks.