Re: Lipid into sphere

From: Ropon-Palacios G. (biodano.geo_at_gmail.com)
Date: Thu Mar 18 2021 - 18:08:32 CDT

One last question dear Jeffrey , packmol can run in parallel?

 

Best,

 

Geo.

 

From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Jeffrey Potoff <jpotoff_at_wayne.edu>
Reply-To: <namd-l_at_ks.uiuc.edu>, Jeffrey Potoff <jpotoff_at_wayne.edu>
Date: Thursday, March 18, 2021 at 5:52 PM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Subject: RE: namd-l: Lipid into sphere

 

If it were me, I would start here:

 

Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types

Jeffery B. Klauda, Richard M. Venable, J. Alfredo Freites, Joseph W. O’Connor, Douglas J. Tobias, Carlos Mondragon-Ramirez, Igor Vorobyov, Alexander D. MacKerell, and Richard W. Pastor

The Journal of Physical Chemistry B 2010 114 (23), 7830-7843

DOI: 10.1021/jp101759q

  

---
Jeffrey Potoff
Interim Chair, Department of Chemical Engineering and Materials Science
College of Engineering
Wayne State University
 
From: Ropon-Palacios G. <biodano.geo_at_gmail.com> 
Sent: Thursday, March 18, 2021 6:48 PM
To: namd-l_at_ks.uiuc.edu; Jeffrey Potoff <jpotoff_at_wayne.edu>
Subject: Re: namd-l: Lipid into sphere
 
Have lipid POPE take from CHARMM-GUI into it and column section named “Surface Area” indicate 58.8 Angstrom^3. This can be right to area per lipid? 
 
From: <owner-namd-l_at_ks.uiuc.edu> on behalf of Jeffrey Potoff <jpotoff_at_wayne.edu>
Reply-To: <namd-l_at_ks.uiuc.edu>, Jeffrey Potoff <jpotoff_at_wayne.edu>
Date: Thursday, March 18, 2021 at 5:28 PM
To: "namd-l_at_ks.uiuc.edu" <namd-l_at_ks.uiuc.edu>
Subject: RE: namd-l: Lipid into sphere
 
If you know the area per lipid for the lipid of interest, couldn’t you calculate the surface area of your sphere and divide by the area per lipid to get the (approximate) number of lipids required? 
 
---
Jeffrey Potoff
Interim Chair, Department of Chemical Engineering and Materials Science
College of Engineering
Wayne State University
 
From: owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> On Behalf Of Ropon-Palacios G.
Sent: Thursday, March 18, 2021 6:19 PM
To: Mike McCallum <mmccallum_at_PACIFIC.EDU>; KS UIUC <namd-l_at_ks.uiuc.edu>
Subject: Re: namd-l: Lipid into sphere
 
[EXTERNAL] 
Yes, but I want calculate number of lipid to placed given an radius of sphere in my case is 425 angstrom 
 
From: Mike McCallum <mmccallum_at_PACIFIC.EDU>
Date: Thursday, March 18, 2021 at 5:13 PM
To: KS UIUC <namd-l_at_ks.uiuc.edu>, "Ropon-Palacios G." <biodano.geo_at_gmail.com>
Subject: Re: namd-l: Lipid into sphere
 
Hi Geo., 
I’d look into PACKMOL.  It should be able to do exactly this for you, and it is easy to use.
 
https://urldefense.com/v3/__http://leandro.iqm.unicamp.br/m3g/packmol/home.shtml__;!!DZ3fjg!uWh88g9gQHZKORAzHObqSSE5sPVsOvNNpjpUZvH_y0zYUTY-bRyfLbwyZybo3gf0Dg$ 
 
Best
Mike
 
On Mar 18, 2021, at 2:25 PM, Ropon-Palacios G. <biodano.geo_at_gmail.com> wrote:
 
Dear NAMD users, 
 
How can calculate lipid (POPE) number to be placed into an sphere the 425 Angstrom. 
 
Best, 
 
Geo. 
 
--
C. Michael McCallum           
Professor                        
Department of Chemistry, UOP    
mmccallum .at. pacific .dot. edu                (209) 946-2636 v  / (209) 946-2607 fax

This archive was generated by hypermail 2.1.6 : Fri Dec 31 2021 - 23:17:11 CST