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

[Justin Lemkul]

On 6/22/17 9:47 AM, gozde ergin 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.
> 

You can't declare force field parameters after you've introduced a 
[moleculetype].  Put it in ffnonbonded.itp or immediately after the #include 
statement for the force field.

-Justin

-- 
==================================================

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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