[gmx-users] Atomtype C not found

Sun Moon sunmoon1360 at yahoo.com
Tue May 7 19:04:27 CEST 2013


Hi
 
I have been using the lipids from Prof Tieleman's website and (using Berger Lipids) in gromacs 4.5.4  I want to try the grompp tool but have encountered this problem:
 
Fatal error:
Atomtype C 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
 
lipid.itpis as the following:
 
[ defaults ]
1       1
[ atomtypes ]
;name     mass     charge ptype  c6           c12
   LO    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carbonyl O, OPLS
  LOM    15.9994    0.000  A 2.36400e-03 1.59000e-06 ;carboxyl O, OPLS
  LNL    14.0067    0.000  A 3.35300e-03 3.95100e-06 ;Nitrogen, OPLS
   LC    12.0110    0.000  A 4.88800e-03 1.35900e-05 ;Carbonyl C, OPLS
  LH1    13.0190    0.000  A 4.03100e-03 1.21400e-05 ;CH1, OPLS
  LH2    14.0270    0.000  A 7.00200e-03 2.48300e-05 ;CH2, OPLS
…
DOPC.itpisas the following:
 [ moleculetype ]
; Name   nrexcl
DOPC     3
[ atoms ]
;   nr    type   resnr  residu    atom    cgnr        charge          mass
     1     LC3       1    DOPC      C1       0         0.4000   15.0350         ; qtot:0.36    
     2     LC3       1    DOPC      C2       0         0.4000   15.0350         ; qtot:0.72 
     3     LC3       1    DOPC      C3       0         0.4000   15.0350         ; qtot:1.08 
     4     LNL       1    DOPC      N4       0        -0.5000   14.0067 ; qtot:0.76 
     5     LH2       1    DOPC      C5       0         0.3000   14.0270         ; qtot:1.0 
     6     LC2       1    DOPC      C6       1         0.4000   14.0270         ; qtot:1.0 
..
DOPC.grofile as the following:
 
128 DOPC in water 
21387
    1DOPC    C1    1   4.048   0.461   2.197 -0.4628 -0.6241 -0.6552
    1DOPC    C2    2   4.064   0.596   2.395 -0.1879  0.0104 -0.0154
    1DOPC    C3    3   4.110   0.366   2.405 -0.5498 -0.8024 -0.0627
    1DOPC    N4    4   4.022   0.466   2.341  0.5789 -0.0490 -0.4766
    1DOPC    C5    5   3.877   0.457   2.361  0.5625  0.0560 -0.5460
    1DOPC    C6    6   3.823   0.315   2.343  0.0671  0.1818 -0.0962
…..
Many thanks for your help in advance!
Sun


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