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 Mon Feb 03 2014 - 06:00:04 PST
