I think it is not trivial trying to make covalent bonds with metals. You
need first to set up distances and constants (K) for components of the
forcefield (see the manual), then you need to define topologies and
charges, well it is not an easy job.
Cesar
Antonio Sergio Kimus Braz escribió:
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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