[gmx-users] ZN HIS binding

[cesar]

I think it is not trivial trying to make covalent bonds with metals. You 
need first to set up distances and constants (K) for components of the 
forcefield (see the manual), then you need to define topologies and 
charges, well it is not an easy job.

Cesar

Antonio Sergio Kimus Braz escribió:
> Hi for all ...
> Can somebody help me, 
> how to make a bonded interaction between
> HIS an Zinc atom ?
>
> I work with a metalloprotease
> and in this protein 3 HIS redisidues make bond with a Zn atom by its NE2 atoms
>
> I try form this bounds by pdb2gmx with option -his
>
> a show only this :
>
> Type a number:1
> Which HISTIDINE type do you want for residue 141
> 0. H on ND1 only (HISA)
> 1. H on NE2 only (HISB)
> 2. H on ND1 and NE2 (HISH)
> 3. Coupled to Heme (HIS1)
>
>
> I need make more one option like Couple to Zinc (HISZ)
>
> I try it :
>
> i insert a line : in specbond.dat in top folder
> HIS	NE2	1	ZIH	ZN	1	0.25	HISZ	ZIH
>
> /in /
> /6/
> CYS	SG	1	CYS	SG	1	0.2	CYS2	CYS2
> CYS	SG	1	HEME	FE	2	0.25	CYS2	HEME
> CYS	SG	1	HEME	CAB	1	0.2	CYS2	HEME
> CYS	SG	1	HEME	CAC	1	0.2	CYS2	HEME
> HIS	NE2	1	HEME	FE	1	0.2	HIS1	HEME
> /HIS	NE2	1	ZIH	ZN	1	0.25	HISZ	ZIH/
>
>
> but it dont resolve my problem
>
> Thanks !
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