[gmx-users] Propylene Carbonate

[Sencer Selcuk]

Sotirios,

Thanks for your response. The angle I am looking at is actually present 
in the molecule, but the corresponding parameters are missing from the 
ffbonded.itp. With the hope that white spaces won't be messed when I 
send this email, this is the propylene carbonate molecule with the 
bonded atom types listed in ffnonbonded.itp:

     O
     ||
     C
    /  \
OS   OS
  |      |
CT---CT-CT


and the angle I cannot find in the ffbonded.itp is OS-C-OS bond.

Best,

Sencer


On Sun, Feb 5, 2017 at 11:18 AM, Sotirios Dionysios I. Papadatos 
<si.papadatos at edu.cut.ac.cy> wrote:
> 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
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