I have a two peptide system with my second chain B having as part of its topology file (and sequence) a Zinc ion. That is, the Zinc ion is literally part of the chain so, that when I generate my itp files using pdb2gmx I get topol_proteinA.itp, topol_proteinB.itp (i.e. no topol_Ion.itp)...I do this because the distance restraint I want is between the Zinc and its coordinated sulfur atoms. I believe I need the Zn and the Cys SG atoms part of the same molecule...here, chainB.
I have read the distance restraint info. in the manual 4.5.4; however, I am still unsure about how to implement it. I have gotten to the point where I use genrestr to generated the itp file having the distance restraint matrix. Now, when I #include this (restraint) file in the topology.top or in the topol_proteinB.itp, I get an error saying that the restraint file is in the wrong location when I use the grompp to make a tpr file.....I have also place in "disre_fc = 1000" in my mdp file.... Can someone be explicit about what I am doing wrong...I did get the "position restraint" to work, but am having trouble here..... Thanks, Steve -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
