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 - 04:00:03 PST
