[gmx-users] The conversion from gromacs to amber

[Mark Abraham]

On 27/01/2012 8:14 AM, Tanping Li wrote:
> Dear gromacs users,
>
> I am a gromacs user, and I am calculating the binding free energy between protein and ligand. A package "sietraj" looks very tempted, which is an alternative of MM-PBSA. However, the prmtop (topology) and trajectory in amber is required.
>
> It is easy to convert gromacs trr to amber trajectory. The conversion from top to prmtop is difficult for me.
> I searched the mailing list and haven't find the way to solve the problem. Can anyone give me some hint of this? I really appreciate your help. I am struggling currently.

Topology conversion utilities are fraught with difficulty to write and 
maintain, so they are rare. You should use the AmberTools to generate 
the topology. Doubtless the sietraj documentation (should) suggest this.

Mark