VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Sun May 10 2009 - 07:00:29 CDT

On Sun, 2009-05-10 at 06:54 +0300, Thomas Evangelidis wrote:
> Dear VMD users,

tom,

> I am resending a message posted in a wrong thread by mistake. I am
> pretty sure the answer will be negative but I just want to give

i don't think that this is the reason for not getting an answer,
i'd rather say, that it is not very clear what you want to do
that thus nobody feels confident to give an answer.

> it a shot. My question is: can I calculate the charges of the residues
> forming the binding cavity only to save some computation time? For

what do you mean by "calculate"? vmd does not compute charges,
it uses the charge information that is stored in a .psf or similar
file and gives that information back to you or uses it for further
calculations (esp).

now if you want to _sum up_ charges, then you can indeed use
selections, but it is not obvious to me what kind of speedup
you are looking for. the sum is an O(n) process and thus even
if done in pure tcl for a large system, usually quite fast.

just very recently two options to do the sum were given here
on this list (off the top of my head, please check with the manual):
vecsum [$sel get charge]
measure sumweights $sel weight charge

HTH,
   axel.

> example can I use the whole structure of the receptor and specify
> those residues, or use a pdb file containing only them (perhaps along
> with the surrounding residues)?
>
> thanks,
> Tom 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
=======================================================================
If you make something idiot-proof, the universe creates a better idiot.