[gmx-users] His protonation and Ligand binding energy evaluation
feenstra at chem.vu.nl
Tue Jun 10 08:59:05 CEST 2003
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).
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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