From: Norman Geist (norman.geist_at_uni-greifswald.de)
Date: Thu Apr 10 2014 - 01:46:05 CDT
As I understand you question, what you need is a "within" selection in
water within 4 of protein
water within 4 of (resid 1 to 5)
(all within 4 of (resid 1 to 5)) and name "CA"
This should give you an impression how it basically works.
PS: This is a VMD question, isn't it?
> -----Ursprüngliche Nachricht-----
> Von: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] Im
> Auftrag von Hongbo Du
> Gesendet: Donnerstag, 10. April 2014 03:22
> An: Boshra Moradi; namd-l_at_ks.uiuc.edu
> Betreff: RE: namd-l: slice of water box
> Hi, Boshra,
> If you want to calculate the interaction energies including non-bonded
> terms between them, you can use the Plugin NAMD Energy available in VMD
> based on the trajectory you have. Remember to update each frame because
> the movability of water molecules around the big molecule.
> Good luck.
> From: Boshra Moradi [boshra.moradi.1983_at_gmail.com]
> Sent: Wednesday, April 09, 2014 5:47 PM
> To: Hongbo Du
> Subject: Re: namd-l: slice of water box
> Hi , Hongbo,
> I want to survey the interactions between atoms of the main molecule
> and water molecules.
> On Thu, Apr 10, 2014 at 3:10 AM, Hongbo Du
> <hongbodu_at_uark.edu<mailto:hongbodu_at_uark.edu>> wrote:
> Hi, Boshra,
> If you just want to get the coordinates of water molecules including
> the big molecule, you can use the ATOM SELECT method in VMD. Please
> check the VMD manual, it is easy to get atoms around the molecule.
> Good luck,
> From: owner-namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu> [owner-
> namd-l_at_ks.uiuc.edu<mailto:owner-namd-l_at_ks.uiuc.edu>] on behalf of
> Boshra Moradi
> Sent: Wednesday, April 09, 2014 5:13 PM
> To: namd-l_at_ks.uiuc.edu<mailto:namd-l_at_ks.uiuc.edu>
> Subject: namd-l: slice of water box
> I have a molecule in a water box.I want to take a slice through the box
> and there will be one or two water molecule layers around that molecule
> .How can i do it?
> I will appreciate very much if
> anyone can give me any advice.
> Thanks in advance,
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