[gmx-users] OPLS definition of Phenyl palmitate

[Ebert Maximilian]

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