[gmx-users] Topology for nBuOH

[Justin A. Lemkul]

Juliana Angeiras wrote:
> 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?
>  

Your directives are out of order.  If you define new atomtypes, etc. they have 
to be defined before they can be used.  See Chapter 5 of the manual.

-Justin

> 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
>  
>  
>  
> 

-- 
========================================

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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