Re: [AMBER] how to add lipid

From: mohammad r <>
Date: Mon, 23 Nov 2015 17:52:41 +0000 (UTC)

Thank you Brian,
I've added the specified numbers of lipid to around the protein by using packmol but when I import the system to the amber and after solvating that with water in tleap (since in the packmol we must specify the number of water molecles and I don't know exactly how many molecules should be added to fill the box entirely, i did the sovation in tleap) the topology file it gives to me is consisted of one mass that is solvated in water and I think there is something wrong. the system must be consisted of three masses, the protein, lipid and water molecules. I didn't use parmEd, I just import the pdb file resulted in packmol to tleap.

    On Monday, November 23, 2015 8:33 PM, Brian Radak <> wrote:

 tleap doesn't currently build lipids at the moment. Two popular tools
are and packmol. The former can also build amber inputs by
running ParmEd as the backend.


On 11/23/2015 11:01 AM, mohammad r wrote:
> Hi every body,

> I’ve got the pdb files of a protein and a lipid, now I want to addspecified concentration of the lipid to the water-protein system but I don’tknow how to do it. I tried the add command but it did not work. I don’t knowwhether for the purpose of adding lipid to the water-protein system the pdbfile of the lipid is necessary or not. Can you please help me?

> Thank you, mohammad.
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Brian Radak
Postdoctoral Scholar
Gordon Center for Integrative Science, W323A
Department of Biochemistry & Molecular Biology
University of Chicago
929 E. 57th St.
Chicago, IL 60637-1454
Tel: 773/834-2812
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Received on Mon Nov 23 2015 - 10:00:02 PST
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