From: Gurunath Katagi (
Date: Mon Feb 06 2012 - 10:37:49 CST

Dear all,

     I want to do a all atomic molecular dynamics simulation of a protein
calbindin using NAMD with CHARMM (v27) (pbdid: 4ICB). in this protein,
there is a link between Calcium ions and few protein atoms/water molecules.
[These bonds are indicated by link section of the pdb file]
but how do i add these links in proteins for simulations.
what patches do i need to apply or are there any parameter files for these
calcium-protein interactions.

or deriving parameters for these bonds by using GAMESS/gaussian is the only
option ..?

please let me know ..

Thank you

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