[gmx-users] Propylene Carbonate
Sencer Selcuk
sselcuk at princeton.edu
Mon Feb 6 15:46:42 CET 2017
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.
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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