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From: Salomon Turgman Cohen (sturgman_at_gmail.com)
Date: Thu Apr 25 2013 - 17:15:20 CDT
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Hmm... acceptorindices and hydrogenindices are empty. How does measure
hbonds know which atom type is hydrogen and which are the donor and
acceptor types?
Salo
On Thu, Apr 25, 2013 at 3:51 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> Hi Salomon,
>
> The most coding-time efficient way of doing this is probably to write out
> all the hbond lists using "measure hbonds", and then parse the result based
> on name or type.
>
> Something like:
>
> set all [atomselect top all]
> set superlist [list [measure hbonds 3.0 30 $all]]
> set donorindices [lindex $superlist 0]
> set acceptorindices [lindex $superlist 1]
> set hydrogenindices [lindex $superlist 2]
> set typelist [$all get type]
> for { set i 0 } { $i < [llength $donorindices] } { incr i } {
> puts "[lindex $typelist [lindex $donorindices $i]] [lindex $typelist
> [lindex $hydrogenindices $i]] [lindex $typelist [lindex $acceptorindices
> $i]] "
> }
>
> Is that what you had in mind?
>
> -Josh Vermaas
>
>
> On 04/25/2013 01:13 PM, Salomon Turgman Cohen wrote:
>
> Hello,
>
> I have the need to detect hydrogen bond like interactions in a system
> consisting of amines and some ions. I was thinking the best way to do this
> is to use the salt-bridges or h-bonds extension but I cannot quite
> understand how to adapt them to my system.
>
> What I would like to do is define a set of donors, hydrogen, and
> acceptors according to their types. So I will give the program something
> like this:
>
> hbonds=((NH3,H3,OO),(NH2,H2,OO),(NH1,H1,OO),...)
>
> In this manner I will tell VMD to look for the those interactions
> according to specific distance and angular cutoffs. What would be the best
> way to implement something like this? Should I work from the current hbond
> plugin and generate my own, or would it be better to write a script from
> scratch? Could I use python scripting? Or would I need the TCL
> functionality in this case?
>
> Salomon
>
> --
> Salomon Turgman Cohen
> Postdoctoral Associate
> Cornell University
> (919) 341-9650
>
>
>
-- Salomon Turgman Cohen Postdoctoral Associate Cornell University (919) 341-9650
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