VMD-L Mailing List

From: Salomon Turgman Cohen (sturgman_at_gmail.com)
Date: Thu Apr 25 2013 - 19:02:36 CDT

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> 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
> > 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>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 <%28919%29%20341-9650>
>>>
>>>
>>>
>>
>>
>> --
>> Salomon Turgman Cohen
>> Postdoctoral Associate
>> Cornell University
>> (919) 341-9650
>>
>
>
>
> --
> Salomon Turgman Cohen
> Postdoctoral Associate
> Cornell University
> (919) 341-9650
>
>
> 

-- 
Salomon Turgman Cohen
Postdoctoral Associate
Cornell University
(919) 341-9650