Hi, I think you have to make this line HIS NE2 1 ZIH ZN 1 0.25 HISZ ZIH as HIS NE2 1 ZIH ZN 3 0.25 HISZ ZIH
because zinc needs to make 3 special bonds. Also check NE2-Zn distances are all within 10% of 0.25 (Assuming you've already defined HISZ and ZIHS in .rtp file.) You also might want to try pdb2gmx without -his option after above modifications. Regards, Ryogo On Mon, 17 Jul 2006 16:21:42 -0300, Antonio Sergio Kimus Braz wrote: > 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 ! > > _______________________________________________ > 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 _______________________________________________ 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
