VMD-L Mailing List

From: Salomon Turgman Cohen (sturgman_at_gmail.com)
Date: Thu Apr 25 2013 - 17:49:44 CDT

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

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