Hi Mohammad,
You might want to consider building your system with Maestro (the free version) and then converting it to an amber compatible system.
Shameless plug, but you can find my tutorial here: https://github.com/ParkerdeWaal/AMBER-Maestro-lipid-tutorial
-----Original Message-----
From: Brian Radak [mailto:brian.radak.accts.gmail.com]
Sent: Monday, November 23, 2015 12:57 PM
To: amber.ambermd.org
Subject: Re: [AMBER] how to add lipid
If you used tleap to solvate (i.e. solvateBox or solvateOct), it expects a single globular solute; I expect this is not what you want. You /might/ be able to trick it into building a box above and below by fiddling with buffer parameters, but that might not give a good structure in the end.
I am not at all familiar with packmol, so I can't really help there.
CharmmGUI handles both lipids around proteins and building water boxes with ions (it uses an elaborate PB MC method). ParmEd would just handle the conversion of those files from the native CHARMM format back to AMBER format.
On 11/23/2015 11:52 AM, mohammad r wrote:
> 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 <brian.radak.accts.gmail.com> wrote:
>
>
> tleap doesn't currently build lipids at the moment. Two popular
> tools are charmmgui.org and packmol. The former can also build amber
> inputs by running ParmEd as the backend.
>
> HTH,
> Brian
>
> 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.
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Tel: 773/834-2812
email: radak.uchicago.edu
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Received on Mon Nov 23 2015 - 10:30:03 PST
