VMD-L Mailing List

From: Nicolas Sapay (nicolas.sapay_at_cermav.cnrs.fr)
Date: Mon Jun 07 2010 - 04:05:01 CDT

Hello,

That's perfect! I had a bit of time to (quickly and dirtily) code the
Cremer-Pople method. I'll do a quick comparison with Hill-Reilly this
week. Ideally, I would like to have as output a string corresponding to
the ring conformation (1C4, 4C1, ...). The values given by Hill-Reilly
do not seem to have a very broad amplitude. As I need to monitor the
conformation of a flexible ring along a MD trajectory, I'm not sure it
is adapted to my needs.

Regards,
Nicolas

John Stone a écrit :
> Hi,
> You can pick 5 and 6 membered rings like this:
> (ringsize 5 from all) or (ringsize 6 from all)
>
> You can also do things with a range of ring sizes, e.g.:
> maxringsize 6 from all
>
> You can also query the Hill-Reilly ring pucker with "$sel get pucker",
> which should only return non-zero values for 5- and 6-membered rings,
> as I recall.
>
> We don't have an atom selection query for Cremer-Pople parameters
> in the atom selection language at present, but in principle it wouldn't
> difficult to add. If people would find this useful, I can put it on the
> TODO list, long though it already is.
>
> Cheers,
> John Stone
> vmd_at_ks.uiuc.edu
>
> On Fri, Jun 04, 2010 at 10:46:30AM +0200, Nicolas Sapay wrote:
>
>> Hello,
>>
>> I need to follow the conformation of a couple of rings (with 5 or 6
>> atoms) over a trajectory. The ring conformation can be visualize with
>> the paper chain representation but I need to put the data in some text
>> file for complementary analysis. Is there a way to get the ring
>> conformation and/or the Cremer-Pople spherical coordinates directly from
>> the paper chain representation? If not, is there at least an easy way to
>> select 5 or 6 membered rings?
>>
>> Regards,
>> Nicolas
>>
>
>
>
>