Error RUNNING GMX_MMPBSA

[Anna VERDINO]

I read in https://valdes-tresanco-ms.github.io/gmx_MMPBSA/dev/howworks/ the section of topology-preparation that in order to run gmx_MMPBSA from file to charmm, the topology must be converted, and the following steps are specified on the site:

>Generates a new index and registers the user-defined groups.
>Generates the pdb of the complex, receptor and ligand.
>Topologies are cleaned (remove water and ions).
>Structures or parameters for the receptor and ligand are generated if it is an ST approximation.
>PBRadii is assigned
>Topologies are converted with parmed or generated with tleap.

Could someone who has already done this kindly tell me what the commands are? What must be written in order to be able to convert the topology?

THANKS IN ADVANCE

ANNA

[Mario Sergio Valdes]

All these steps are taken care of by gmx_MMPBSA. That section tries to show the user how it works so that it is not a black box and can understand what we do.

The index file and groups are user-defined, but this step is necessary for MD simulation, so you must know how to do it.