Hi for all ... Can somebody help me, how to make a bonded interaction between HIS an Zinc atom ?
I work with a metalloprotease and in this protein 3 HIS redisidues make bond with a Zn atom by its NE2 atoms I try form this bounds by pdb2gmx with option -his a show only this : Type a number:1 Which HISTIDINE type do you want for residue 141 0. H on ND1 only (HISA) 1. H on NE2 only (HISB) 2. H on ND1 and NE2 (HISH) 3. Coupled to Heme (HIS1) I need make more one option like Couple to Zinc (HISZ) I try it : i insert a line : in specbond.dat in top folder HIS NE2 1 ZIH ZN 1 0.25 HISZ ZIH in 6 CYS SG 1 CYS SG 1 0.2 CYS2 CYS2 CYS SG 1 HEME FE 2 0.25 CYS2 HEME CYS SG 1 HEME CAB 1 0.2 CYS2 HEME CYS SG 1 HEME CAC 1 0.2 CYS2 HEME HIS NE2 1 HEME FE 1 0.2 HIS1 HEME HIS NE2 1 ZIH ZN 1 0.25 HISZ ZIH but it dont resolve my problem Thanks !
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