Re: Spherical restraints

From: Giacomo Fiorin (giacomo.fiorin_at_gmail.com)
Date: Tue Apr 06 2021 - 10:06:58 CDT

Hello Yasser, there are a few things to check, but the first one would be
to make sure that you actually loaded that configuration. There will be a
(fairly verbose) set of messages printed when you do.

What you did there is setting a string variable "config" to contain the
configuration text, which can be used in a Tcl script but you actually need
to load it afterwards, e.g.:

cv config ${config}

On Tue, Apr 6, 2021 at 10:09 AM Almeida-Hern√°ndez, Yasser, Dr. <
yasser.almeida-hernandez_at_uni-due.de> wrote:

> Hello,
>
>
> I want to spherically restrain a ligand around a Cu2+ cation with harmonic
> walls. For this, I am using the colvars module as:
>
>
> # Restraint the ligand in a sphere of r=15 AA around the Cu2+
> set config "
>
> colvars on
>
> colvar {
> name LIG_sphere
> distance {
> group1 {atomNumbers 704} # Cu2+ cation
> group2 {atomNumbersRange 707-734} # Ligand
> }
> }
>
> harmonicWalls {
> name LIG_sphere
> colvars HL
> outputEnergy on
> lowerWalls 0
> upperWalls 15
> forceConstant 1000
> }
> "
>
>
> ... but it doesn't work. The ligand tumbles all around.
>
>
> Am I missing something? Any help will be appreciated.
>
>
> Best,
>
> Yasser
>
>
> --
> Dr. Yasser Almeida-Hernandez
> Postdoctoral Researcher
> Computational Biochemistry group
> T01 R03 D45
> Faculty of Biology
> University of Duisburg-Essen
> Universitätsstr. 2, 45117 Essen
> Email: yasser.almeida-hernandez_at_uni-due.de
> <%20yasser.almeida-hernandez_at_uni-due.de>
> Phone: +49 201 183 2457 <+49%20201%20183%202457>
>
>

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