Thank you Charles and Repic;
I was used to use CHARMM-GUI to simulate the lipid bilayer with amembrane-bound protein. But I don't know how I can simulate a box with a protein in center and lipids around it and the box is solvated with water. Is it really possible? If yes, which section in the website does it?
Best, Mohammad.
On Friday, August 28, 2015 1:46 AM, Repic Matej <matej.repic.epfl.ch> wrote:
Perhaps you might want to try CHARMM-GUI? It will pack the specified
amount of any conceivable mixture of lipids and water around your peptide
and provide you with all the files and scripts to run the simulations with
CHARMM or AMBER.
Best,
Matej
------------------------------------------------------
Dr. Matej Repic
Ecole Polytechnique Fédérale de Lausanne
Laboratory of Computational Chemistry and Biochemistry
SB - ISIC – LCBC
BCH 4108
CH - 1015 Lausanne
------------------------------------------------------
On 8/27/15, 19:22, "Charles Lin" <clin92.ucsd.edu> wrote:
>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.
>>
>
>Is 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 Fri Aug 28 2015 - 00:30:03 PDT
