Re: [AMBER] how to add lipid

From: Charles Lin <clin92.ucsd.edu>
Date: Thu, 27 Aug 2015 17:22:14 +0000

You would probably want to fill it with packmol first or you can use the solvatebox command to fill it with water.
________________________________________
From: mohammad r [mohammad.r0325.yahoo.com]
Sent: Wednesday, August 26, 2015 7:17 AM
To: AMBER Mailing List
Subject: Re: [AMBER] how to add lipid

Thank you Charles for your help;
If I use setbox can I fill it with solvent? If yes how? I don't know the command.
Best, M.


     On Wednesday, August 26, 2015 12:46 AM, Bill Ross <ross.cgl.ucsf.edu> wrote:


 Trial and error.. also note that the box will shrink with equilibration because there are vdw voids in the initial placement.

You could equilibrate your box without lipid, then remove the water, place with packmol, and write a program to remove the overlapping waters (unless packmol will do it). Remember, the box will shrink after every substitution or addition owing to the vdw voids created.

Bill

<div>-------- Original message --------</div><div>From: mohammad r <mohammad.r0325.yahoo.com> </div><div>Date:08/25/2015 3:43 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
</div>Indeed I don't know how to generate a fixed box of water around the lipid-peptide which is generated by packmol.



    On Tuesday, August 25, 2015 2:58 PM, mohammad r <mohammad.r0325.yahoo.com> wrote:


I found it. tleap cannot recognize the water molecules, because when I generated the pdb file consisting of the protein and the lipids around it by packmol then imported it to the tleap, it could read it and there I solvated my system by water with solvatebox command. But there I have a problem again, as I want to add specified amount of lipids to my system (e.g. 10mM) and I don't know the dimensions of my system till the last level and these dimensions are changed as I change the numbers of lipids surround the peptide in packmol ( because I use solvatebox command for solvating water), so I cannot specify how many lipids I have to add in packmol ( to reach the specified molarity).



    On Tuesday, August 25, 2015 1:07 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:


Looks like it isn't a pdb file - how about pasting a few lines here.

Bill

<div>-------- Original message --------</div><div>From: mohammad r <mohammad.r0325.yahoo.com> </div><div>Date:08/24/2015 11:14 PM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
</div>the error is like this:
Creating new UNIT for residue: CLA sequence: 7622
Created a new atom named: CLA within residue: .R<CLA 7622>
Creating new UNIT for residue: CLA sequence: 7623
Created a new atom named: CLA within residue: .R<CLA 7623>
  total atoms in file: 22939
  Leap added 208 missing atoms according to residue templates:
      208 H / lone pairs
  The file contained 22738 atoms not in residue templates



    On Tuesday, August 25, 2015 9:13 AM, mohammad r <mohammad.r0325.yahoo.com> wrote:


Thank you Bill;
Before I use the loadpdb, I load leaprc.ff14SB, frcmod.ionsjc_tip3p, leaprc.lipid14 force fields.I've read the leap tutorial but still I don't know which section you mean. Do you know any other turorials?Also, is there another way to generate the solvated system except packmol? Maybe it would help.
Best, M.




    On Monday, August 24, 2015 11:50 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:


So you have to find or build residue templates and load them before loadpdb. Have you studied the tutorials yet? They are good for this. By now you should also have found papers by people who have done this in Amber to get the parameters at least.

Bill

<div>-------- Original message --------</div><div>From: mohammad r <mohammad.r0325.yahoo.com> </div><div>Date:08/24/2015 10:44 AM (GMT-08:00) </div><div>To: AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] how to add lipid </div><div>
</div>No it cannot recognize the residues in the pdb file


    On Monday, August 24, 2015 10:11 PM, Jason Swails <jason.swails.gmail.com> wrote:


On Mon, Aug 24, 2015 at 1:28 PM, mohammad r <mohammad.r0325.yahoo.com>
wrote:

> I tried loadpdb, but it couldnot read it.
>

‚ÄčIs it a PDB file?? If loadPDB doesn't read it, there is probably
something wrong with the PDB file and it violates the PDB standard in some
way.

--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 27 2015 - 10:30:03 PDT
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