AMBER Archive (2004)

Subject: Re: AMBER: How to make leap recognise Zn2+?

From: Guanglei Cui (cuigl_at_csb.sunysb.edu)
Date: Tue Jul 06 2004 - 08:58:27 CDT

Hi,

As far as I know, Zn parameters have been included in parm99.dat and
parm99EP.dat. If you go to $AMBERHOME/dat/leap/parm, 'grep -iw zn
parm*.dat" and you will see Zn^2+ van der waals parameters are there.
You'll have to decide the atomic charges suitable for your system. You
may want to check out the literature for MD simulations of zinc
containing proteins.

Guanglei

Yongzhi Chen wrote:
>
> Could you give me further direction? Thanks a lot.
>
> Another thing I worried about happened in residue 431 and 450. From the
> remarks in the 3BTA.pdb, I known that residue 432-449 were not located
> in the experiment and the residue 431 have missing atoms CG CD NE CZ NH1
> NH2 and residue 450 have missing atoms CG OD1 ND2. As I already found,
> when I loaded the 3BTA.pdb into tleap. Tleap would add these missing
> atoms automatically. As I understood, this protein is a di-chain one
> linked by a disulfide bond (residue 429-residue453). In this case,
> should I add a ¡°TER¡± cards between the residue 431 and residue 450
> lines? I found if I do in that way, tleap would add one more atom OXT.
> Which method is right?
>
>
>
> Yongzhi
>
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