[gmx-users] making topology file manually

[Justin Lemkul]

On 6/7/16 12:49 PM, Mohsen Ramezanpour wrote:
> Dear All,
>
> I am trying to insert a 5-atom ring composed of carbon and non-carbon atoms
> in the middle of my small molecule.
>
> Reading literature, I have got confused a bit. Especially about the
> "pairs", "exclusions", and "improper dihedrals" sections in topology file.
>
> Is anyone aware of any step-by-step tutorial for manually making a topology
> file for a small molecule from scratch, or modifying it manually? I
> appreciate it in advance for letting me know.
>

The specific details depend on the force field, which means you need to know all 
the gory details of how the force field works.  Exclusions are generally 
anything within 3 bonds, and that's what the GROMACS nrexcl value does, so you 
don't have to set anything explicitly unless you've got something funny going 
on.  Pairs are 1-4 interactions; different force fields treat these differently. 
  Impropers keep planar groups planar.  Not all force fields use impropers, or 
perhaps use them sparsely and generally rely on proper dihedrals to control 
out-of-plane wagging motion.  Depends on the group, depends on 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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