[gmx-users] The conversion from gromacs to amber

Tanping Li jia_11_osu at yahoo.com
Thu Jan 26 22:14:32 CET 2012

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.


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