[gmx-users] Atomtype OW not found

Sun Moon sunmoon1360 at yahoo.com
Sat May 11 11:37:43 CEST 2013


Hi,
I am doing pure membrane simulation in DOPC environment (using Berger
Lipids) in Gromacs 4.0.7  I want to try the grompp tool but have
encountered this problem:
 
Fatal error:
Atomtype OW  not found
 
Topology file is as
the following:
#include "lipid.itp"
#include "dopc.itp"
#include "spc.itp"
#include "ions.itp"
'[ system ]'
; name
DOPC bilayer in water
'[ molecules ]'
; name  number
DOPC      128
SOL       4825
……………….
Inlipid.itp file, lipid-SPC/SPCE interactions is defined:
;;
lipid-SPC/SPCE interactions
   LO    OW    1 2.50200e-03  2.06700e-06
  LOM    OW    1 2.50200e-03  2.06700e-06         
  LNL    OW    1 2.98000e-03  3.25900e-06
   LC    OW    1 3.59800e-03  6.04400e-06
  LH1    OW    1 3.26800e-03  5.71200e-06
  LH2    OW    1 4.30700e-03  8.17000e-06
   LP    OW    1 4.92600e-03  8.21000e-06
  LOS    OW    1 2.60500e-03  2.24100e-06
…….
Spc.itpfile from gromos
FF as the following:
[ moleculetype ]
; molname        nrexcl
SOL                2
[ atoms ]
;   nr   type  resnr residue  atom   cgnr     charge       mass
     1     OW      1    SOL     OW      1      -0.82
     2     HW      1    SOL    HW1      1       0.41
     3     HW      1    SOL    HW2      1       0.41
…
…………………….
dopc.groas the following:
….
129SOL     OW 6913   4.231   0.169   1.664 -0.1323 -0.0792  0.5040
 129SOL    HW1 6914   4.146   0.202   1.704 -0.3042  0.1272 -0.0232
 129SOL    HW2 6915   4.263   0.089   1.715 -0.7744 -0.3135  0.5523
 130SOL     OW 6916   4.513   4.020   6.355  0.3593 -0.2561  0.3581
  130SOL    HW1 6917   4.591   3.980   6.403 -0.2604 -0.1715  1.4756
  130SOL    HW2 6918   4.545   4.090   6.291  1.1718  0.0930  1.1277
……..
What should I do?
 
Regards,
Sun


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