[gmx-users] Urea topology problem

Rebeca García Fandiño regafan at hotmail.com
Thu Dec 18 15:10:03 CET 2008

I would like to simulate a proteína in urea, using Gromacs. I have tried to use the box included in Gromacs by default (urea+h2o.gro and urea.itp). 
The topology of the urea/water-solvated protein is:

; Include forcefield parameters
#include "ffG43a2.itp"

#include "protein.itp"

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
; Include water and urea topology
#include "urea.itp"
#include "spc.itp"
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct       fcx        fcy        fcz
   1    1       1000       1000       1000
[ system ]
; Name
Protein in water/urea
[ molecules ]
; Compound        #mols
Protein             1
UREA        426
SOL         5885
 When I try
 grompp -f min.mdp -c solvated_urea.gro -p solvated.top -o min.tpr
I get these errors:
ERROR 1 [file solvated.top, line 39]:
  atom C1 (Res UREA-1) has mass 0
ERROR 2 [file solvated.top, line 39]:
  atom O2 (Res UREA-1) has mass 0
ERROR 3 [file solvated.top, line 39]:
  atom N3 (Res UREA-1) has mass 0
ERROR 4 [file solvated.top, line 39]:
  atom H4 (Res UREA-1) has mass 0
ERROR 5 [file solvated.top, line 39]:
  atom H5 (Res UREA-1) has mass 0
ERROR 6 [file solvated.top, line 39]:
  atom N6 (Res UREA-1) has mass 0
ERROR 7 [file solvated.top, line 39]:
  atom H7 (Res UREA-1) has mass 0
ERROR 8 [file solvated.top, line 39]:
  atom H8 (Res UREA-1) has mass 0
Which force field does this urea.itp correspond to? Where should it look for the atomtypes of urea?
Thank you very much for your help,
Rebeca Garcia
Parc Cientific de Barcelona
regafan at hotmail.com
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