Hi Stephane,
I think I understand what's going on here. Indeed, when you use the
solvateBox command, it must be inserting only partial phospholipids around
your protein structure. It must be inserting lipids without taking into
account the Lipid11 connectivity.
Lipid11 is structured such that the phospholipids are divided into three
"residues" with connect0 and connect1 atoms that join the molecule.
The solvateBox command did not anticipate this case and I don't know of an
easy solution within LEaP. LEaP would have to recognize the connectivity
before the solvateBox command is used.
You'll need to remove the extra lipid residues somehow. It's possible to
search for these unconnected residues by looking at the connectivity, but
that would not be easy. It'd probably faster to manually remove them.
VMD could be an option here. I have not tried to solvate a protein with a
lipid bilayer with VMD, but I imagine it could be done. Then the
charmmlipid2amber.x script can convert your system to a PDB to be read by
LEaP.
The alternatives are to use a web based option. I've used CHARMM-GUI and
our charmmlipid2amber.x script works with that. I have not tested
membuilder.
All the best,
Ben Madej
Walker Molecular Dynamics Lab
On Tue, Feb 11, 2014 at 7:43 AM, Stéphane Azoulay <s.azoulay.unistra.fr>wrote:
> 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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> > > > AMBER.ambermd.org
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Received on Tue Feb 11 2014 - 15:00:03 PST
