From: Salomon Turgman Cohen (sturgman_at_gmail.com)
Date: Thu Apr 25 2013 - 19:12:09 CDT

Never mind. I understand.

Salo

On Thu, Apr 25, 2013 at 8:02 PM, Salomon Turgman Cohen
<sturgman_at_gmail.com>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>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
>

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