[Dock-fans] HEM in DOCK 6

Scott Brozell sbrozell at scripps.edu
Wed Nov 7 09:37:10 PST 2007


Asked and answered in Chimera-users; see this thread:


On Tue, 6 Nov 2007, snoze pa wrote:

> Hi, I am new in this mailing list but found chimera more useful than any
> other software. I was building a protein that contain HEME. When I was
> calculating the charge using chimera interface, then it is asking for
> HEM[FE] and HEM[nonFE] formal charge. I know chimera is using MMTK and AMBER
> forcefield. If I will give the default value then it is assigning +2 charge
> to Fe, which is not a match based on AMBER forcefield.  Meanwhile I try to
> change the Formal charge manually, but still it gives the same +2 for Fe.
> Anybody used chimera to prepare a protein having heme for dock or geometry
> build.
>  My another question is: Is it possible in chimera to merge non polar
> hydrogen charges on the heavy atoms, the technique used in autodock.
> I will highly appreciate your help and suggestions in this matter.
> thanks in advance.

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