[gmx-users] Propylene Carbonate

Justin Lemkul jalemkul at vt.edu
Mon Feb 6 15:54:29 CET 2017 


On 2/6/17 9:46 AM, Sencer Selcuk wrote:
> Justin,
>
> I am pretty sure there is a reliable parametrization of propylene carbonate (PC)
> in OPLSaa. The OPLSaa parameters included in GROMACS lists all PC atoms
> explicitly as well. The opls_771 to opls_779 non-bonded types correspond to PC
> atoms.
>
> In the bonded part, however, OS-C-OS angle is missing. I checked the parameters
> provided with Tinker, the same angle is missing.  There are several papers &
> dissertations where people say they used GROMACS and the OPLS parameters
> provided there in to model PC. So I feel like none of the parameters are
> missing, but  I am doing something wrong.
>

Contact those authors and ask for their topologies to see what they did.  Maybe 
they parametrized the angle and just forgot to mention that, or they used 
parameters from a similar angle (and forgot to mention that), or they used 
different types.  But if simulations of this molecule have been done before, 
avoid reinventing the wheel - this is why there are corresponding authors!

-Justin

> I would really appreciate if you, or someone with experience can take a quick
> look -as I believe this should be a very straight forward example of .top
> generation.
>
> Best,
>
> Sencer
>
>
> On Mon, Feb 6, 2017 at 7:41 AM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>> On 2/5/17 12:29 PM, Sencer Selcuk wrote:
>>> 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.
>>>
>>
>> If the force field doesn't already have parameters for it, you'll need to
>> parametrize it in accordance with the parent force field's normal
>> parametrization strategy.  There may be parameters in OPLS-AA that are
>> published but not incorporated in GROMACS; there have been several recent
>> extensions of the force field for drug-like molecules that may be useful.
>>
>> -Justin
>>
>>> 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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>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>
>> Department of Pharmaceutical Sciences
>> School of Pharmacy
>> Health Sciences Facility II, Room 629
>> University of Maryland, Baltimore
>> 20 Penn St.
>> Baltimore, MD 21201
>>
>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>> http://mackerell.umaryland.edu/~jalemkul
>>
>> ==================================================
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>> Gromacs Users mailing list
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==================================================

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