[gmx-users] Distance Restraints

Steve Seibold stevesei at ymail.com
Thu May 7 19:57:38 CEST 2015

 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


More information about the gromacs.org_gmx-users mailing list