[gmx-users] Topology for nBuOH

[Juliana Angeiras]

Hi,

I'm trying to include parameters of n-butanol in the topology file (below) (i'm 
not using opls or other force field for butanol), but when i run the grompp 
program, I obtain the following message:

Fatal error:
Atomtype Hb not found

How can I fix this problem?

Thanks

Topology file:

; Include forcefield parameters      
#include "oplsaa.ff/forcefield.itp"  
         
; Include forcefield parameters      
#include "oplsaa.ff/tip5p.itp"       
[ moleculetype ]
; name  nrexcl 
BuOH 3       
 [ atoms ]              
;   nr    type   resnr  residu    atom    cgnr        charge          mass
     1      Hb  1   BuOH     HO     1       0.38       1.0080
     2      O   1   BuOH     OH     1      -0.66      15.9994
     3      C   1   BuOH     CA     1       0.40      12.0110
     4      C   1   BuOH     CB     1      -0.22      12.0110
     5      C   1   BuOH     CC     1      -0.22      12.0110
     6      C   1   BuOH     CD     1      -0.33      12.0110
     7      H   1   BuOH     HA     1      -0.06       1.0080
     8      H   1   BuOH     HB     1      -0.06       1.0080
     9      H   1   BuOH     HC     1       0.11       1.0080
     10     H   1   BuOH     HD     1       0.11       1.0080
     11     H   1   BuOH     HE     1       0.11       1.0080
     12     H   1   BuOH     HF     1       0.11       1.0080
     13     H   1   BuOH     HG     1       0.11       1.0080
     14     H   1   BuOH     HF     1       0.11       1.0080
     15     H   1   BuOH     HG     1       0.11       1.0080
 [ atomtypes ]
; name   at.num   mass   charge   ptype   V(c6)   W(c12)
   Hb  1     1.0080     0.38   A   0.4149611E-07  0.9737356E-04
   O   8    15.9994    -0.66   A   0.9722461E-06  0.1247853E-02
   C   6    12.0110     0.40   A   0.4895634E-05  0.2791672E-02
   C   6    12.0110    -0.22   A   0.4895634E-05  0.2791672E-02   
   C   6    12.0110    -0.33   A   0.4895634E-05  0.2791672E-02
   H   1     1.0080    -0.06   A   0.4415162E-06  0.5131711E-03
   H   1     1.0080     0.11   A   0.4415162E-06  0.5131711E-03
 [ bondtype ]                
;  ai   aj funct           c0           c1          
   HB  O   1   0.10900   462750.4             
   O   C   1   0.14300   376560.0          
   C   C   1   0.15300   265265.6         
   H   C   1   0.10800   284512.0
 [ angletype ]              
;  ai    aj    ak func           c0        c1        
  C    O    HB  1    108.000    460.240         
  C    C    O   1    108.000    418.400         
  C    C    C   1    112.000    488.273         
  H    C    H   1    109.470    292.000
 [ dihedrals ]            
  1  2  3  4  3    0.41840   1.25520   0.00000  -1.67360   0.00000   0.00000
  2  3  4  5  3    2.87441   0.58158   2.09200  -5.54799   0.00000   0.00000
  3  4  5  6  3    2.92880  -1.46440   0.20920  -1.67360   0.00000   0.00000
 [ nonbond_params ]
; i   j   func   V(c6)   W(c12)
  H   H   1      0.4149611E-07  0.9737356E-04
  H   HW  1      0.4149611E-07  0.9737356E-04
  H   C   1      0.4415162E-06  0.5131711E-03
  H   O   1      0.1927397E-06  0.3416812E-03
  H   OW  1      0.1927397E-06  0.3416812E-03
  H   Hb  1      0.4149611E-07  0.9737356E-04
  HW  HW  1      0.0000000E+00  0.0000000E+00
  HW  C   1      0.4415162E-06  0.5131711E-03
  HW  O   1      0.0000000E+00  0.0000000E+00
  HW  OW  1      0.0000000E+00  0.0000000E+00
  HW  Hb  1      0.4149611E-07  0.9737356E-04
  C   C   1      0.4895634E-05  0.2791672E-02
  C   O   1      0.2159724E-05  0.1866537E-02
  C   OW  1      0.2159724E-05  0.1866537E-02
  C   Hb  1      0.4415162E-06  0.5131711E-03
  O   O   1      0.9722461E-06  0.1247853E-02
  O   OW  1      0.1562282E-05  0.1785000E-02
  O   Hb  1      0.0000000E+00  0.0000000E+00
  OW  OW  1      0.2510400E-05  0.2552000E-02
  OW  Hb  1      0.0000000E+00  0.0000000E+00
  Hb  Hb  1      0.4149611E-07  0.9737356E-04
 [ system ]
 ; Name
 BuOH in water
 [ molecules ]
 ; Compound        #mols
 BuOH               343
 SOL                185
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