[gmx-users] ethanol bond types

[nishap.patel at utoronto.ca]

Quoting David van der Spoel <spoel at xray.bmc.uu.se>:

> On 3/3/10 8:14 PM, nishap.patel at utoronto.ca wrote:
>> Hello,
>>
>>    I am trying to simulate Ethanol in water using OPLSAA. I already  
>>  tried it with all atoms, but now I want to try it with United  
>> atoms  for ethanol, i.e. CH3,CH2,OH, and HO in my topology file. I  
>> created  the topology but I got an error saying 'No bond types', so  
>> I  checked ffoplsaabon.itp file, and as the error indicated I could  
>>  not find any bond types. Is there a way for me to determine the   
>> bonds? This is my topology file for ethanol:
>>
>> [ moleculetype ]
>> ; Name            nrexcl
>> Ethanol             3
>>
>> [ atoms ]
>> ;   nr       type  resnr residue  atom   cgnr     charge       mass  
>>   typeB    chargeB      massB
>>     1   opls_068      1    EOH     CB      1          0     15.035   
>>   ; qtot 0
>>     2   opls_081      1    EOH     CA      2      0.265     14.027   
>>   ; qtot 0.265
>>     3   opls_078      1    EOH     OH      2       -0.7    15.9994   
>>   ; qtot -0.435
>>     4   opls_079      1    EOH     HO      2      0.435      1.008   
>>   ; qtot 0
>>
>> [ bonds ]
>> ;  ai    aj funct            c0            c1            c2            c3
>>    1     2     1
>>    2     3     1
>>    3     4     1
>>
>> [ pairs ]
>> ;  ai    aj funct            c0            c1            c2            c3
>>    1     4     1
>>
>> [ angles ]
>> ;  ai    aj    ak funct            c0            c1            c2    
>>          c3
>>    1     2     3     1
>>    2     3     4     1
>>
>> [ dihedrals ]
>> ;  ai    aj    ak    al funct            c0            c1            
>>   c2            c3            c4            c5
>>    1     2     3     4     3
>>
>> I checked one of the paper that has been published using the same   
>> parameters as follows:
>>
>>   Table 1. Potential Parameters and Molecular
>>         Geometries of OPLS-UA and SPC/E
>>                                             qa
>> atom or group       ?, Å      , kJ/mol
>>                         OPLS
>>     R1            3.905      0.7322        0.000
>>     R2            3.905      0.4937        0.265
>>                                          -0.700
>>     O             3.070      0.7113
>>     H             0.000      0.0000        0.435
>>
>> I would really appreciate some suggestions, on how I should tackle   
>> the error.
>>
>> Thanks
>>
>> Nisha P
>>
>>
> The united atom parameters are really leftovers from long past.
> Jorgensen published his first all-atom alcohol simulations in 1988
> IIRC. There is a methanol paper from 1983. Just search literature for
> Jorgensen, methanol ethanol and it will show up. Then you will to type
> in the parameters yourself, see chapter 5.
>
> -- 
> David.
>
Thanks David. These are the parameters I added. Do you think they seem  
reasonable?

[ bondtypes ]
; i    j  func       b0          kb
C3    C2      1    0.15300   259400.0
C2    OH      1    0.14300   267800.0


[ angletypes ]
;  i    j    k  func       th0       cth
   C3     C2     OH      1   108.00     100.000   ;
   C2     OH     HO      1   108.50     110.000

[ dihedraltypes ]
;  i    j    k    l   func     coefficients
C3  C2  OH  HO  3  0.00000   3.49000   0.00000   3.13000   0.00000   0.00000

And this is the topology file I created using the parameters and  
pdb2gmx command:

; Include forcefield parameters
#include "ffoplsaa.itp"

[ moleculetype ]
; Name            nrexcl
Ethanol             3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass   
typeB    chargeB      massB
      1   opls_068      1    EOH     CB      1          0     15.035   ; qtot 0
      2   opls_081      1    EOH     CA      2      0.265     14.027    
; qtot 0.265
      3   opls_078      1    EOH     OH      2       -0.7    15.9994    
; qtot -0.435
      4   opls_079      1    EOH     HO      2      0.435      1.008   ; qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
     1     2     1
     2     3     1
     3     4     1

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
     1     4     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2       
       c3
     1     2     3     1
     2     3     4     1

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1             
c2            c3            c4            c5
     1     2     3     4     3

Thanks

-Nisha


________________________________________________________________________
> David van der Spoel, PhD, Professor of Biology
> Dept. of Cell and Molecular Biology, Uppsala University.
> Husargatan 3, Box 596,  	75124 Uppsala, Sweden
> phone:	46 18 471 4205		fax: 46 18 511 755
> spoel at xray.bmc.uu.se	spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
>
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Nisha Patel
MSc Candidate
Leslie Dan Faculty of Pharmacy
Department of Pharmaceutical Sciences
144 College Street
Room 1172
Toronto, ON
M5S 3M2
Canada
Telephone: 416-978-1536