VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Apr 25 2013 - 17:39:51 CDT

Oh boo... I really should learn to test these things first, lest I
mislead people too far. The second line should be:
set superlist [measure hbonds 3.0 30 $all]
since measure hbonds already returns a list, and making a list out of a
list just makes things confusing.
-Josh Vermaas

On 04/25/2013 05:15 PM, Salomon Turgman Cohen wrote:
> 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
> <mailto: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 <tel:%28919%29%20341-9650>
>
>
>
>
> --
> Salomon Turgman Cohen
> Postdoctoral Associate
> Cornell University
> (919) 341-9650