[gmx-users] non-bonded sigma for amino nitrogen–carboxylate oxygen interactions in OPLSAA in GROMACS

Thu Jun 22 15:54:50 CEST 2017

Thank Justin.
Mark you are right. I did not think about to check the manual. 

Thanks again.
> On 22 Jun 2017, at 15:51, Mark Abraham <mark.j.abraham at gmail.com> wrote:
> 
> Hi,
> 
> I'd start by looking in the documentation. Section 5.3.2 of the manual
> clearly suggests putting it in the ffnonbonded.itp file, which is where you
> expected to find it at the start of this thread, right? :-)
> 
> Mark
> 
> On Thu, Jun 22, 2017 at 3:47 PM gozde ergin <gozdeeergin at gmail.com <mailto:gozdeeergin at gmail.com>> wrote:
> 
>> Hey Justin,
>> 
>> I figured out how they calculated the sigma values.
>> Basically they just take the geometric mean of nitrogen and oxygen sigma
>> and epsilon from ffnonbed.itp file in OPLS-AA force field
>> and calculated the pairwise LJ for N-O interaction.
>> 
>> Now I also try to add this information in my topol.top file.
>> In order to do that as you have mentioned I added a section ,
>> 
>> [ nonbond_params ]
>> ; i     j       func    sigma   epsilon
>> opls_287  opls_272  1  0.323161248385416  0.790543521382599
>> 
>> 
>> after [ atoms ] section however I am facing with an error :
>> 
>> Fatal error:
>> Syntax error - File topol.top, line 42
>> Last line read:
>> '[ nonbond_params ]'
>> Invalid order for directive nonbond_params
>> 
>> Any suggestion would be appreciated.
>> 
>>> On 21 Jun 2017, at 16:46, Justin Lemkul <jalemkul at vt.edu> wrote:
>>> 
>>> 
>>> 
>>> On 6/21/17 10:39 AM, gozde ergin wrote:
>>>> Hi MArk,
>>>> Thanks for the respond. I understood that point however I still do not
>> get which sigma to change.
>>>> I the paper JCTC 2017, Miller et. al. they have mentioned that they
>> increase the for nitrogen–carboxylate oxygen interactions in OPLSAA.
>>>> However there are two sigma in oplsaa.ff/ffnonbonded.itp one for amino
>> notrogen and one for carboxylate oxygen.
>>>> 
>>       sigma            epsilon
>>>> opls_287   N3   7  14.00670    -0.300       A    3.25000e-01
>> 7.11280e-01
>>>> opls_272   O2   8  15.99940    -0.800       A    2.96000e-01
>> 8.78640e-01
>>>> Which one defines the amino nitrogen–carboxylate oxygen interactions?
>>>> Which sigma should I change?
>>> 
>>> What people are doing more and more is introducing pair-specific
>> parameters to override the combination rule values.  That's likely what is
>> being referred to. OPLS-AA by default does not use pair-specific LJ
>> interactions, hence why you find no [nonbond_params] in ffnonbonded.itp.
>> The same is true of AMBER.  CHARMM uses some (also called NBFIX in the
>> literature), while GROMOS uses a ton of these.
>>> 
>>> To override the LJ combination rules, add a [nonbond_params] directive
>> with the published parameters, which refer to an *interaction*, not an atom
>> type.
>>> 
>>> -Justin
>>> 
>>>> Thanks
>>>>> On 21 Jun 2017, at 16:21, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>>>> 
>>>>> Hi,
>>>>> 
>>>>> Different force fields work differently and thus are implemented
>>>>> differently. Look at oplsaa.ff/ffnonbonded.itp and you will see that
>> sigma
>>>>> is a property of the atomtype
>>>>> 
>>>>> Mark
>>>>> 
>>>>> On Wed, Jun 21, 2017 at 4:16 PM gozde ergin <gozdeeergin at gmail.com>
>> wrote:
>>>>> 
>>>>>> Dear users,
>>>>>> 
>>>>>> I am trying to change the sigma value of amino nitrogen–carboxylate
>> oxygen
>>>>>> interactions in OPLSAA in GROMACS.
>>>>>> However I have difficulties to understand which parameter i should
>> change
>>>>>> in ffnonbonded.itp file?
>>>>>> I am looking something like [ nonbond_params ] section however it is
>> not
>>>>>> exist in ffnonbonded.itp?
>>>>>> Any help would be appreciated.
>>>>>> 
>>>>>> Thanks in advance.
>>>>>> --
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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 <mailto:jalemkul at outerbanks.umaryland.edu> <mailto:
>> jalemkul at outerbanks.umaryland.edu <mailto:jalemkul at outerbanks.umaryland.edu>> | (410) 706-7441
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