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

[gozde ergin]

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> | (410) 706-7441
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