[gmx-users] Distance Restraints

Diogo Vila Viçosa diogo.vicosa at fc.ul.pt
Fri May 8 11:43:31 CEST 2015

Dear Steve,

First of all you should take a look in all mdp options regarding distance
I am not 100% familiar with dist res in version 4.5.4 but without
"dirse=simple" for example I think you will not have any distance
restraints because you will be using the default value which is "disre=no"
I guess.

Regarding the location of the distance restraints it can be placed after
all the parameters of your molecule. Otherwise I think grompp will give an

Finally, and probably the main reason for my reply, I wonder if what you
want is a distance restraints or an actual bond between the Zn and the S
atoms (four I guess).

Diogo Vila Viçosa

Em qui, 7 de mai de 2015 às 18:58, Steve Seibold <stevesei at ymail.com>

>  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
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