Oh yes, very good, I will take a look to this option.
Thank you very much, have a nice day.
Stephane
On Tue, 2014-02-11 at 14:00 +0000, ABEL Stephane 175950 wrote:
> Stephane
>
> An additional approach is to use VMD and the membrane plug-in [1] in your desktop. The (mixed) membrane can be generated separately with Membuilder [2] (an web server). MemBuilder can be used to construct simulate membrane with AMBER (at this moment Slipid)
>
> [1] http://www.ks.uiuc.edu/Research/vmd/plugins/membrane/
> [2] http://bioinf.modares.ac.ir/software/mb/
>
> I hope you have all the tools for your simulations
>
>
>
> --------
> Stéphane Abel, PhD
> CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> Bat 528 Porte 11
> Gif-sur-Yvette, F-91191 FRANCE
> Phone (portable) : +33 6 49 37 70 60
> ________________________________________
> De : Stéphane Azoulay [s.azoulay.unistra.fr]
> Date d'envoi : mardi 11 février 2014 14:44
> À : amber.ambermd.org
> Objet : Re: [AMBER] RE : Protein insertion into a membrane
>
> A lot means I don't know yet, maybe 5 maybe 10 or more...
> I just wanted to have this membrane ready to be used on my computer
> instead of having to go on a website that can be sometimes overwhelmed
> by too many users or whatever.
> It's ok I will do it with CHARMM-GUI and see later.
>
> Anyway, thank you for help.
>
> Stéphane A.
>
> On Tue, 2014-02-11 at 11:41 +0000, ABEL Stephane 175950 wrote:
> > Ok I understand.
> >
> > "A lot" means 5, 10 or more simulations? CHARMM-GUI is relatively fast to construct a mixed bilayer and insert membrane proteins (say less than 1 hours/system) This is much faster than MD simulations ;). So you could write a flexible script than only reorder and rename the lipids whatever is your system. Be aware that after the membrane insertion, you will need to equilibrate your system, so I think it is worth a try. My $0.02
> >
> > Stéphane
> >
> > --------
> > Stéphane Abel, PhD
> > CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> > Bat 528 Porte 11
> > Gif-sur-Yvette, F-91191 FRANCE
> > Phone (portable) : +33 6 49 37 70 60
> > ________________________________________
> > De : Stéphane Azoulay [s.azoulay.unistra.fr]
> > Date d'envoi : mardi 11 février 2014 12:05
> > À : amber.ambermd.org
> > Objet : Re: [AMBER] Protein insertion into a membrane
> >
> > Hi Stéphane,
> >
> > Thank you for your reply.
> > Actually, I will have to do md simulations on a lot of membrane proteins
> > so I'd like to create a mixed membrane with CHARMM-GUI and to insert the
> > protein into the membrane by myself with tleap. It will be faster than
> > using CHARMM-GUI for constructing all the systems membrane+protein for
> > each protein.
> >
> > Stéphane A.
> >
> > On Tue, 2014-02-11 at 10:51 +0000, ABEL Stephane 175950 wrote:
> > > Hello Stéphane
> > >
> > > Why not to use CHARMM-GUI to constuct your membrane and insert your protein into the bilayer? After these step, you will need to write a little script to reorder the phospholipid headgroups and alkyl chains and rename the atoms according to the AMBER rules. By doing this, you will not encounter this problem.
> > >
> > > Stéphane
> > >
> > > --------
> > > Stéphane Abel, PhD
> > > CEA Saclay DSV/IbItec-S/SB2SM & CNRS UMR 8221
> > > Bat 528 Porte 11
> > > Gif-sur-Yvette, F-91191 FRANCE
> > > Phone (portable) : +33 6 49 37 70 60
> > > ________________________________________
> > > De : Stéphane Azoulay [s.azoulay.unistra.fr]
> > > Date d'envoi : mardi 11 février 2014 09:51
> > > À : amber.ambermd.org
> > > Objet : Re: [AMBER] Protein insertion into a membrane
> > >
> > > Hi,
> > >
> > > Nobody has dealt with this problem before?
> > > If this is the case do you know a way to create a phospholipid bilayer
> > > (with different types of phospholipid and cholesterol) solvated in water
> > > and ions, in which i can insert a membrane protein?
> > >
> > > Thank you for your help,
> > >
> > > Stephane Azoulay
> > > PhD Student
> > > Strasbourg University
> > >
> > > >Dear Amber community,
> > > >
> > > >I would like to create a phospholipidic bilayer membrane that can be
> > > >used for molecular dynamics of different transmembrane proteins.
> > > >
> > > >To do this, I have followed the instructions of the Amber lipid force
> > > >field tutorial
> > > >( http://ambermd.org/tutorials/advanced/tutorial16/An_Amber_Lipid_Force_Field_Tutorial.html ).
> > > >
> > > >I have used the CHARMM-GUI website to generate a membrane of 256 DOPC
> > > >(128 up and 128 down so I have 256 PC heads and 512 OL tails).
> > > >
> > > >My problem is during the insertion of the protein into the membrane
> > > >using tleap : after insertion, the number of OL tails is not equal to
> > > >twice the number of PC heads.
> > > >
> > > >Here are the commands I run in tleap :
> > > >
> > > >> # Load force fields
> > > >> source leaprc.ff03.r1
> > > >> source leaprc.lipid11
> > > >>
> > > >> # Load the protein
> > > >> Prot = loadpdb Protein.pdb
> > > >>
> > > >> # Load the membrane
> > > >> Mb = loadpdb Membrane.pdb
> > > >>
> > > >> # Check and neutralize the protein
> > > >> check Prot
> > > >> charge Prot
> > > >> addIons2 Prot Cl- 0
> > > >>
> > > >> # Insert the protein into the membrane and create a periodic box
> > > >> solvateBox Prot Mb {15 4 25} 0.75
> > > >> setbox complex vdw
> > > >>
> > > >> # Save in pdb format and topology and coordinate files
> > > >> savepdb Prot Prot_in_Mb.pdb
> > > >> saveamberparm Prot Prot_in_Mb.top Prot_in_Mb.inpcrd
> > > >>
> > > >> quit
> > > >
> > > >
> > > >I get this message after the last command :
> > > >
> > > >> saveamberparm Prot Prot_in_Mb.top Prot_in_Mb.inpcrd
> > > >Checking Unit.
> > > >Building topology.
> > > >Building atom parameters.
> > > >Building bond parameters.
> > > >Building angle parameters.
> > > >Building proper torsion parameters.
> > > >Building improper torsion parameters.
> > > > total 1398 improper torsions applied
> > > >Building H-Bond parameters.
> > > >Not Marking per-residue atom chain types.
> > > >Marking per-residue atom chain types.
> > > > (Residues lacking connect0/connect1 -
> > > > these don't have chain types marked:
> > > >
> > > > res total affected
> > > >
> > > > CCYS 1
> > > > CHIE 1
> > > > CPRO 1
> > > > NASP 1
> > > > NPRO 1
> > > > NSER 1
> > > > OL 254
> > > > PC 139
> > > > WAT 6849
> > > > )
> > > >
> > > >So I have 139 PC heads and 254 OL tails. (139*2=278 =! 254)
> > > >
> > > >When I look to the pdb file Prot_in_Mb.pdb (with Sybyl software), the
> > > >head are not linked to the tails, some phospholipids surrounding the
> > > >protein do not have two OL tails but just one and some OL tails are
> > > >alone without any PC head around...
> > > >
> > > >I think that when inserting the protein into the membrane, the lipids
> > > >OL-PC-OL are not joined so one OL is removed (or one OL and PC)
> > > >instead
> > > >of removing the whole phospholipid.
> > > >
> > > >Could you please help me to solve this problem?
> > > >
> > > >Stephane
> > >
> > > _______________________________________________
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Received on Tue Feb 11 2014 - 08:00:02 PST
