[gmx-users] making topology file manually

[Mohsen Ramezanpour]

Thanks Justin,

This is why I have got confused then, as each force field treats them in a
different way.

Knowing the details of force field seems necessary then. As another
solution to this:

Can we just make the topology file using some web servers or software (ATB,
SwissParam, Antechamber, PRODRG, ...) and trust the output and continue
with?

By "trust" I literally mean to:
1) not be worry about the assigned lines (atom types, as well as bonds,
angels, dihedrals, impropers, and pairs between these atom types) in the
topology file as recognised by the above mentioned tools
AND
2) check for the correct numbers of assigned lines based on information in
force field files (ffbonded, ffnonbonded) and of course validating the
simulation results

Best,
Mohsen

On Tue, Jun 7, 2016 at 6:33 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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