[gmx-users] Propylene Carbonate

[Sencer Selcuk]

Dear all,

I am coming from a first principles background to the classical MD 
world, and up until now I used only ReaxFF implementation in LAMMPS 
which doesn't really require a topology file of all bonds and angles 
etc. Now I would like to do some OPLSaa simulations, starting with 
liquid propylene carbonate. That is partly because of a scientific 
problem I am interested in, and partly I thought it would be easy to 
work with as oplsaa.ff/atomtypes.atp explicitly include the atoms of 
propylene carbonate (opls_771 to opls_779).

I tried using topolbuild to generate an initial topology file. It 
correctly guessed the correct opls_nnn names most of the atoms. For the 
others the atom type (CT, C, O etc.) were correct, and I am providing 
charges from literature, so I suppose it wouldn't matter (is that 
right?). Still, I changed the opls_nnn names to the correct ones listed 
in atomtypes.atp.

My real problem is that one of the angles, OS-C-OS angle, seems to be 
missing from the force field files. gmx grompp complains about it (and 
about 4 dihedrals, actually) saying:

> ERROR 1 [file molecule.top, line 95]:
>   No default Angle types
> 
> 
> ERROR 2 [file molecule.top, line 100]:
>   No default Proper Dih. types
> 
> 
> ERROR 3 [file molecule.top, line 101]:
>   No default Proper Dih. types
> 
> 
> ERROR 4 [file molecule.top, line 102]:
>   No default Proper Dih. types
> 
> 
> ERROR 5 [file molecule.top, line 103]:
>   No default Proper Dih. types

I am copying the relevant parts about the missing angle, and the mdp, 
gro and top files are attached:


> [atoms]
>    10    opls_773     1        PC      OS    3  -0.44200  15.99940    
>    ;   0.1370000
>    11    opls_772     1        PC       C    4   0.85700  12.01100    
>    ;   0.9940000
>    12    opls_771     1        PC       O    4  -0.51000  15.99940    
>    ;   0.4840000
>    13    opls_773     1        PC      OS    2  -0.48400  15.99940    
>    ;   0.0000000
> ...
> [angles]
> ...
>     10    11    13                                 ;    OS-     C-    
> OS


I have inspected the ffbonded.itp file manually, and parameters for 
OS-C-OS angle is not listed. There is a OS-CO-OS listing, which I 
understand belongs to acetal like structures. Shall I use this -as I 
have seen numerous literature examples where people say "we used OPLSaa 
force field" to describe propylene carbonate, without giving any 
details. I am pretty sure, the problem is not about the force field 
file itself, it is not missing a line or anything like that - I also 
looked at the oplsaa parameteres of Tinker, and parameters for the same 
angle is missing in that case as well. Then what do I do with the 
missing dihedrals (it is the whole first dihedrals section in the .top 
file)?

Finally, the .top file generated by topolbuild has other lines with 
"missing" data, as well. But I can find the relevant parameters in the 
ffbonded.itp file, and grompp does not complain anyway. So can I 
suppose it is going to use the correct parameters for these lines?

> 
>      7     5     6    1     110.700    313.8000     ;    CT-    CT-   
>  HC
>      7     5    13   1     109.500    418.4000     ;    CT-    CT-    
> OS
>      5   13    11                                                  ;  
>   CT-    OS-     C ;  data missing
>      5     7    10   1     109.500    418.4000     ;    CT-    CT-    
> OS
>      5     7     8    1     110.700    313.8000     ;    CT-    CT-   
>  HC
>      5     7     9    1     110.700    313.8000     ;    CT-    CT-   
>  HC

I really appreciate any help as a novice here! Best,

Sencer Selcuk
Department of Chemistry
Princeton University
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