[gmx-users] Propylene Carbonate

[Sotirios Dionysios I. Papadatos]

automated builders usually produce these mistakes. I see that you already checked which atoms correspond to this error. Check first if there is an actual bond there. If it is check ffbonded if these atom types are parametrized.

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Sencer Selcuk <sselcuk at princeton.edu>
Sent: Wednesday, February 1, 2017 6:18:07 AM
To: gromacs.org_gmx-users at maillist.sys.kth.se
Subject: [gmx-users] Propylene Carbonate

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