Res: Res: [gmx-users] Topology for nBuOH

Justin A. Lemkul jalemkul at vt.edu
Wed Jul 13 19:04:02 CEST 2011



Juliana Angeiras wrote:
> Hi Justin,
>  
> Sorry if I am slow to understand these things, but I really want to use 
> gromacs for simulate my system: butanol-water mixture in several 
> concentrations, using tip3p for water and include the parameters for 
> butanol and for water-butanol intermolecular interactions. Everything I 
> tried until now didn't work. First, I did what you suggest: I have 
> changed the order for [ nonbond_params ] putting it before the directive 
> [ moleculetype ], but the answer of grommp was that HW (tip3p) atom is 
> not recognized. Then I have changed the position of the "includes" to 

You can't define a molecule before you define the parameters that are to be 
applied to it.  The force field level must take precedence over the molecule level.

> top of the archive, but the new message of the grompp was that invalid 
> order for  [ defaults ], that seems obviously for me because is already 
> exist in the include archives. Then, I have removed the directive 
> defaults, but the new message was that the atomtype order is invalid. My 
> question is what is the correct order for these things.
>  

The required order of directives is in Table 5.4 (and then 5.5 and 5.6) of the 
manual.  In your case, you need to have something along the lines of:

#include "oplsaa.ff/forcefield.itp" ; [ defaults ] is here

; After this are your custom entries - note that spelling matters!
; Your previous messages used e.g. "bondtype" and "angletype"
; which are not valid identifiers.
[ atomtypes ]
...
[ bondtypes ]
...
[ angletypes ]
...
[ nonbond_params ]
...

#include "oplsaa.ff/tip3p.itp"

After that list the parameters for n-butanol and finish with [ system ] and [ 
molecules ] directives to describe the content of the system.

-Justin

> Thanks for your help,
>  
> Juliana Angeiras B. da Silva.
> Laboratório de Química Teórica e Computacional
> Departamento de Química Fundamental
> Universidade Federal de Pernambuco
> Recife, PE - Brasil.
>  
> The last archive.top:
> ; Include forcefield parameters     
> #include "oplsaa.ff/forcefield.itp"
> ; Include forcefield parameters     
> #include "oplsaa.ff/tip3p.itp"      
>  
> ; [ defaults ]
> ; nbfunc        comb-rule       gen-pairs       fudgeLJ fudgeQQ
> ;   1     3    yes    0.5    0.5
>  
>  [ 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
>  
>  [ 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
>  
> [ 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           
>  
>  [ 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
>  
>  [ system ]
>  ; Name
>  BuOH in water
>  
>  [ molecules ]
>  ; Compound        #mols
>  BuOH               343
>  SOL                185
> 
> ------------------------------------------------------------------------
> *De:* Justin A. Lemkul <jalemkul at vt.edu>
> *Para:* Discussion list for GROMACS users <gmx-users at gromacs.org>
> *Enviadas:* Quarta-feira, 13 de Julho de 2011 12:10:03
> *Assunto:* Re: Res: [gmx-users] Topology for nBuOH
> 
> 
> 
> Juliana Angeiras wrote:
>  > Hi,
>  >  really the problem was with the order, but now i have another 
> problem (below). I have already read the chapter 5, but i didn't fix my 
> problem. I would like to use an archive .itp for the butanol, although i 
> use the tip3p for water in the system (mixture water-butanol), I want 
> use different parameters for nonbonded interactions between 
> water-butanol (because were parametrized specifically for these 
> interactions). How can I do that? My atual archive .top is more below.
>  > 
> 
> Again, your directives are out of order.  The [nonbond_params] are part 
> of the top-level force field definition and thus must come before the 
> molecule definitions.
> 
> -Justin
> 
>  > Archive .top:
>  >  [ defaults ]
>  > ; nbfunc        comb-rule      gen-pairs      fudgeLJ fudgeQQ
>  >    1    3    yes    0.5    0.5
>  >  [ 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
>  >  [ 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            [ 
> 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
>  >  ; Include forcefield parameters      ;#include 
> "oplsaa.ff/forcefield.itp"  ; Include forcefield parameters    #include 
> "oplsaa.ff/tip3p.itp"        [ 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
>  >  Error with grompp:
>  >  WARNING 1 [file BuOHaa.top, line 27]:
>  >  Overriding atomtype C
>  >
>  > WARNING 2 [file BuOHaa.top, line 28]:
>  >  Overriding atomtype C
>  >
>  > WARNING 3 [file BuOHaa.top, line 30]:
>  >  Overriding atomtype H
>  >
>  > ERROR 1 [file BuOHaa.top, line 32]:
>  >  Invalid directive bondtype
>  >
>  > WARNING 4 [file BuOHaa.top, line 34]:
>  >  Too few parameters on line (source file toppush.c, line 246)
>  >
>  > WARNING 5 [file BuOHaa.top, line 35]:
>  >  Too few parameters on line (source file toppush.c, line 246)
>  >
>  > WARNING 6 [file BuOHaa.top, line 36]:
>  >  Too few parameters on line (source file toppush.c, line 246)
>  >
>  > WARNING 7 [file BuOHaa.top, line 37]:
>  >  Too few parameters on line (source file toppush.c, line 246)
>  >
>  > ERROR 2 [file BuOHaa.top, line 39]:
>  >  Invalid directive angletype
>  >
>  > WARNING 8 [file BuOHaa.top, line 41]:
>  >  Too few parameters on line (source file toppush.c, line 315)
>  >
>  > WARNING 9 [file BuOHaa.top, line 42]:
>  >  Too few parameters on line (source file toppush.c, line 315)
>  >
>  > WARNING 10 [file BuOHaa.top, line 43]:
>  >  Too few parameters on line (source file toppush.c, line 315)
>  >
>  > WARNING 11 [file BuOHaa.top, line 44]:
>  >  Too few parameters on line (source file toppush.c, line 315)
>  > Generated 10 of the 10 non-bonded parameter combinations
>  > Generating 1-4 interactions: fudge = 0.5
>  > Generated 10 of the 10 1-4 parameter combinations
>  > -------------------------------------------------------
>  > Program grompp, VERSION 4.5.4
>  > Source code file: toppush.c, line: 1166
>  > Fatal error:
>  > Atomtype opls_111 not found
>  > Thanks,
>  >  Juliana Angeiras B. da Silva.
>  > Laboratório de Química Teórica e Computacional
>  > Departamento de Química Fundamental
>  > Universidade Federal de Pernambuco
>  > Recife, PE - Brasil.
>  >
>  > ------------------------------------------------------------------------
>  > *De:* Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>  > *Para:* Discussion list for GROMACS users <gmx-users at gromacs.org 
> <mailto:gmx-users at gromacs.org>>
>  > *Enviadas:* Terça-feira, 12 de Julho de 2011 12:42:49
>  > *Assunto:* Re: [gmx-users] Topology for nBuOH
>  >
>  >
>  >
>  > 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
>  >
>  > ========================================
>  > -- gmx-users mailing list    gmx-users at gromacs.org 
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> -- ========================================
> 
> 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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-- 
========================================

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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