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, -- Tarak -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Only plain text messages are allowed! * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
