[gmx-users] metal ligand bond

tarak karmakar tarak20489 at gmail.com
Sat Jul 28 19:43:33 CEST 2012

Dear All,

   The protein with which I'm working with, contains Zn metal and it
has tetrahedral coordination site. There are HISTIDINE side chains
within distance ~ 2.3 to 2.4 . So my questions are as follows

(1) In that distance range there is no possibility to form a covalent
bond between Zn and Nitrogen of the HISTIDINE side chain. So how can I
model the interaction between the metal and the histidine nitrogen ?
Should I keep the Zn(II) ion as isolated metal center ?

(2) At pH 5.00 HISTIDINE side chain should be protonated. So when  a
proton has been placed in between the metal center and the histidine
nitrogen [Zn-H-N-his system ] then Zn-H distance is coming about ~1.0
or below. After minimization HISTIDINE is moving far from the metal
center. Then should I remove the protonated hydrogen of that
particular HISTIDINE residue ?

(3) Should I fix the metal position during the equilibration run [short NVT] ?

Sorry for lot of queries .
Thanks in advance,


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