[gmx-users] how to set Restraints

[Justin Lemkul]

Please be sure to keep the discussion on the mailing list.

On 2/20/16 8:54 AM, Sana Saeed wrote:
> thank you for explaining. i studied manual and understood restraints. but i
> don't know how to get phi dphi and other parameters, is there any formula or
> tool to get these values.

phi = the value you want to preserve
dphi = how much that value is allowed to vary before the restraint kicks in

Normally, dihedral restraints are used to preserve some experimentally known 
ensemble of structures, so dphi can be obtained from the observed values.  In 
the case where you're just using dihedral restraints to preserve the pose, I 
don't know of any real firm rules in how you choose the value.  Probably you can 
obtain a reasonable guess from a normal, unbiased simulation of the complex. 
You want to be obtaining the binding free energy using only realistic poses, so 
the level of realism here is dictated by the force field and its resulting 
configurations.

-Justin

> Sana Saeed Khan,
> Teaching-Research Assistant
> Chemoinformatics Lab
> Graduate Student, MS bioinfo
> Department of Bioinformatics
> Soongsil University, Seoul, South Korea.
>
>
> On Friday, February 19, 2016 6:11 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>
>
>
> On 2/18/16 9:11 PM, Sana Saeed wrote:
>  > hisir Justin Lemkul  and gmx usersi am stuck in a problem. i am performing MD
>  > simulation of complex of protein and ligand for binding free energy
>  > calculation. i have done all the basics of MD, performed all the BEVANLAB
>  > tutorials for my learning and some other papers examples. but i never dealt
>  > with binding free energy calculations , so in different tutorials they have
>  > the complex topology, which is my problem, i made ligand and protein
>  > topologies but now i dont know how to get distance, dihedral and angle
>  > restraints, Sir Justin Lemkul you replied me "To include intermolecular
>  > restraints and bonded terms, just use [intermolecular_interactions] at the
>  > end of the .top (available in versions 5.1 and newer).  Use global atom
>  > numbers to define the interactions." can you a little bit explain how to do
>  > that.Thanks in advance
>
> It's exactly the same as any interaction.  In the .top file:
>
> [ system ]
> ...
> [ molecules ]
> ...
> [ intermolecular_interactions ]
> [ dihedrals ]
> i j k l (parameters) <- here, i-j-k-l are global atom numbers taken from the
> coordinate file
>
>
> -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 <mailto:jalemkul at outerbanks.umaryland.edu> |
> (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
>
> ==================================================
>
>

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

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

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