VMD-L Mailing List

From: Luis Gracia (lug2002_at_med.cornell.edu)
Date: Fri Sep 30 2005 - 15:07:22 CDT

Hi!

Ok, I am not sure if it is what you need, but this is what I have. It
calculates between molecules and/or frames: a) rmsd in terms xyz,
distance between atoms, angles or dihedrals (as defined in labels), and
b) number of contacts and hbonds (as defined in vmd).

For each type of analysis you request the plugin creates an object (2D
matrix representation) which is clikable and interacts with vmd, showing
the corresponding representation. These objects can also be combined, i.
e., sum of two objects.

It is still under development, but I'll be happy to share it with you.
If somebody else wants to try it, please write me. I have added a little
preview here:
http://physiology.med.cornell.edu/faculty/hweinstein/vmdplugins/rmsdtt/rmsdtt2.html

Suggestion are wellcome.

Best,

Luis

Luis Gracia, PhD
Department of Physiology & Biophysics
Weill Medical College of Cornell University
1300 York Avenue, Box 75
New York, NY 10021

Tel: (212) 746-6375
Fax: (212) 746-8690
lug2002_at_med.cornell.edu

Charles McCallum said the following on 09/30/05 10:14:
> Hey, that's great, I appreciate it!
>
>
> Cheers,
>
> Mike
> On Sep 29, 2005, at 9:27 PM, Luis Gracia wrote:
>
>
>> Hi!
>>
>> I have a tool that can do that with dihedrals in general, I'll try to
>> post it tomorrow.
>>
>> Best,
>>
>> Luis
>>
>> Charles McCallum wrote:
>>
>>
>>> Hi there, I was wondering if anyone had a script to calculate RMSD
>>> of dihedrals (say, psi and phi, though general would work also), or
>>> alternatively, how to use the RMSD menu tool to achieve the same
>>> results? I'm hoping to avoid doing it myself, but if I have to...
>>> Thanks,
>>> Mike
>>> --
>>> C. Michael McCallum http://chemistry.cop.uop.edu/
>>> cmccallum.html
>>> Associate Professor Department of Chemistry,
>>> UOP mmccallum .at. pacific .dot. edu (209)
>>> 946-2636 v / (209) 946-2607 fax
>>>
>>>
>>
>>
>>
>
> --
> C. Michael McCallum http://chemistry.cop.uop.edu/ cmccallum.html
> Associate Professor
> Department of Chemistry, UOP
> mmccallum .at. pacific .dot. edu (209) 946-2636 v /
> (209) 946-2607 fax
>