VMD-L Mailing List

From: Joao Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Mon Sep 16 2019 - 09:35:59 CDT

Hi Ashma,

 

The qwikmd_* macros that you see in VMD were meant to be used by QwikMD as internal definitions of the molecule types.

 

Regarding your specific case, you can try to use exwithin instead of within. This keyword will exclude the molecules that you are defining as a reference, e.g., protein. For more sophisticated selections, you can include your primary selection between parenthesis, and then add “and not …”.

 

I hope this helps.

 

Best,

 

João

 

 

 

From: <owner-vmd-l_at_ks.uiuc.edu> on behalf of Ashma Khan <ashmakhan200_at_gmail.com>
Date: Monday, September 16, 2019 at 4:52 AM
To: <vmd-l_at_ks.uiuc.edu>
Subject: vmd-l: For calculating the number of osmolytes molecules

 

Dear Sir,

I want to calculate the osmolyte molecules at certain distance from the protein surface. So, I use qwikmd_hetero within 5 of protein, but I get osmolyte molecules as well as some protein molecules also in every frames.Please provide me suitable solution for calculating only osmolyte molecules