[gmx-users] ZN HIS binding

[Ryogo Sugitani]

Hi,

I think you have to make this line
HIS     NE2     1       ZIH     ZN      1       0.25    HISZ    ZIH
as
HIS     NE2     1       ZIH     ZN      3       0.25    HISZ    ZIH

because zinc needs to make 3 special bonds.
Also check NE2-Zn distances are all within 10% of 0.25
(Assuming you've already defined HISZ and ZIHS in .rtp file.)
You also might want to try pdb2gmx without -his option
after above modifications.

Regards,

Ryogo

On Mon, 17 Jul 2006 16:21:42 -0300, Antonio Sergio Kimus Braz wrote:
> 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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