[gmx-users] OPLS definition of Phenyl palmitate

[Ebert Maximilian]

Hi,

a small little update. I saw that CT OS C_2 O_2 and CT OS C_2 CT are defined OPLS/AA. I used these parameters now to define CA OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. Any thoughts on that? I really have difficulties to visualize dihedral angles and I am not sure if this would actually give roughly the same geometry or not.

Thanks and have a good weekend.

Max

> On Jun 5, 2015, at 4:38 PM, Ebert Maximilian <m.ebert at umontreal.ca> wrote:
> 
> Dear list,
> 
> I ran into some problem to define the topology of phenyl palmitate. My main problem is a missing dihedral angle definition in OPLS/AA. Here is a sketch of the molecule without hydrogen (I hope it turns out to be readable in the email):
> 
> 
>                                      O17
>                                       ||
>    C21 - C20                 C16     (C)n
>   /                \               /     \      /   \
> C22              C19 - O18      C15    C1
>   \                /
>    C23 - C24
> 
> I think I defined the atom types correctly:
> 
> [ atoms ]
> ;   nr  type  resi  res  atom  cgnr     charge      mass   
>     1 opls_768     1   PNR   C22    4    -0.1952     12.01100  
>     2 opls_145     1   PNR   C21    5    -0.0500     12.01100  
>     3 opls_145     1   PNR   C20    6    -0.1550     12.01100 
>     4 opls_145     1   PNR   C23    7    -0.0500     12.01100   
>     5 opls_145     1   PNR   C24    8    -0.1550     12.01100   
>     6 opls_472     1   PNR   C19    9     0.1591     12.01100 
>     7 opls_473     1   PNR   O18   10    -0.3732     15.99940   
>     8 opls_465     1   PNR   C16   11     0.6491     12.01100    
>     9 opls_466     1   PNR   O17   12    -0.5100     15.99940   
>    10 opls_136     1   PNR   C15   13    -0.1264     12.01100 
>    11 opls_136     1   PNR   C14   14    -0.0804     12.01100
>    12 ….
> 
> The problem is now in the ester since there is no dihedral definition of CA OS C_2 O_2 and CA OS C_2 CT in OPLS/AA. I assigned C19 the atom type 472 which is Cipso phenyl ester with type CA and hence O18 473 (AA -OR phenyl ester). Do I understand 472 correctly? How can I resolve the missing two dihedral angles? 
> 
> I also wanted to know if somebody has an idea what is meant by: AA C:   esters - for R on C=O, use #280-#282 of the atom type opls_465. Do I need in this case to assign opls_280 to C15 and opls_282 to the corresponding hydrogens since they are the R of the ester?
> 
> Thank you very much for your advice,
> 
> Max
> 
> 
> 
> 
> 
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