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 - 03:00:03 PST
