[gmx-users] His protonation and Ligand binding energy evaluation

[Anton Feenstra]

Jorge Hernanez Fernandez wrote:
> Hello dear GROusers!:
> 
>         I’m some kind of new GROMACS user and only in a week I fall in big
> troubles!  Working in a complex Prot-ZN (Zn coordinated by 2 His) my GRO
> (Gromacs FF), making the .gro file assumes that my coordinating His is type A
> or B automatically. How I can change the A or B types of His in
> Zn-coordinating His?? It’s important because in 100 ps MD one of my His is
> going away from coordination zone due to a big N-H in the wrong place!!!
> Second: How I can evaluate the (TOTAL) interaction energy between Prot-Ligand
> across the MD?? 
> Thanks in advance:

IIRC, pdb2gmx has the option '-his' (check correct spelling), to allow you
to set the Histidine type 'interactively'.

Energies you can get from g_energy (or you could use g_lie but there are
some bugs in that one, check the lists archive).


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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