[gmx-users] ligand topology building.

[Justin Lemkul]

On 11/4/19 2:07 AM, Yogesh Sharma wrote:
> hello users
>
> I am using ATB server for ligand topology development.  there is a section
> named FORMAt having options GROMACS, GROMAC11, GROMAC96 and LAMPP  what
> does it mean? and in  files section there is choice  for Topology Files and
> structure files as following
>
> GROMACS G54A7FF All-Atom (ITP file)
>
> GROMACS G54A7FF United-Atom (ITP file)
>
> Structure Files
>
> All-Atom PDB (optimised geometry)
>
> United-Atom PDB (optimised geometry)
>
> United-Atom PDB (original geometry)
>
> All-Atom PDB (original geometry)
>
>   what are the best option to proceed with, avoiding artifacts?

Is GROMOS a united-atom or all-atom force field?

-Justin

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Justin A. Lemkul, Ph.D.
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