[gmx-users] metal ligand bond
tarak20489 at gmail.com
Sat Jul 28 19:43:33 CEST 2012
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,
More information about the gromacs.org_gmx-users