[gmx-users] ZN HIS binding

[raja]

Hi,
Try to use nonbonded harmonic potential term (bond type 6) with Kb value
of 1673.6 KJ/mol nm2. I tried this value and it worked good for my
simulation , please try a trail run and see for whether it restraints
the crystallographic distances ,if yes can use it for your simulation. 
Regards,
B.Natarj

On Mon, 17 Jul 2006 16:21:42 -0300, "Antonio Sergio Kimus Braz"
<askbraz2list at gmail.com> said:
> 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 !
-- 
  raja
  raja_28 at fastmail.us

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