[Dock-fans] HEM in DOCK 6

snoze pa snoze.pa at gmail.com
Tue Nov 6 08:04:02 PST 2007


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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