Hi, Try to use nonbonded harmonic potential term (bond type 6) with Kb value of 1673.6 KJ/mol nm2. I tried this value and it worked good for my simulation , please try a trail run and see for whether it restraints the crystallographic distances ,if yes can use it for your simulation. Regards, B.Natarj
On Mon, 17 Jul 2006 16:21:42 -0300, "Antonio Sergio Kimus Braz" <[EMAIL PROTECTED]> said: > 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 ! -- raja [EMAIL PROTECTED] -- http://www.fastmail.fm - A fast, anti-spam email service. _______________________________________________ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
