VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Apr 25 2013 - 17:53:44 CDT

Don't need to guess, it's in the docs. :D
http://www.ks.uiuc.edu/Research/vmd/current/ug/node136.html
The output is actually D A H, which is why I was somewhat sly and
reordered the print statement in the loop to match what you wanted.
-Josh

On 04/25/2013 05:49 PM, Salomon Turgman Cohen wrote:
> OK. Fixed it by replacing:
>
> set superlist [list [measure hbonds 3.0 30 $all]]
>
> with:
>
> set superlist [measure hbonds 3.0 30 $all]
>
> I am guessing that the output is D H A?
>
> -s-
>
>
>
> On Thu, Apr 25, 2013 at 6:15 PM, Salomon Turgman Cohen
> <sturgman_at_gmail.com <mailto:sturgman_at_gmail.com>> 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 <tel:%28919%29%20341-9650>
>
>
>
>
> --
> Salomon Turgman Cohen
> Postdoctoral Associate
> Cornell University
> (919) 341-9650