VMD-L Mailing List

From: Josh Vermaas (vermaas2_at_illinois.edu)
Date: Thu Apr 25 2013 - 19:07:30 CDT

Hi Salomon,

My understanding is that under the hood the hbonds plugin does the exact
same thing (calls measure hbonds once per frame, then formats the output
in a way the authors thought was useful). I've had some success with the
detailed h-bonds description, but it is very detailed, and sometimes
difficult to convolve into useful insights.
-Josh

On 04/25/2013 07:02 PM, Salomon Turgman Cohen wrote:
> Hey Josh,
>
> Thanks a lot. I can easily process this list to get what I need. I
> guess I need to ask what is the difference between this and the hbonds
> plugin? Is there any?
>
> Salomon
>
>
> On Thu, Apr 25, 2013 at 6:53 PM, Josh Vermaas <vermaas2_at_illinois.edu
> <mailto:vermaas2_at_illinois.edu>> wrote:
>
> 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 <tel:%28919%29%20341-9650>
>
>
>
>
> --
> Salomon Turgman Cohen
> Postdoctoral Associate
> Cornell University
> (919) 341-9650