Hi Fabian,
If your membrane is entirely DOPC lipid then the membrane will be neutral. DOPC is zwitterionic (net neutral) so you do not need to add charge neutralising ions for the membrane. You may however choose to add a salt concentration to the water layer.
I believe your procedure should work - you can ignore the split warnings. You do not need neutralising ions for the membrane, just the protein.
Check that the solvateBox step does not add water within the membrane region - I normally keep the water layer from the charmm GUI membrane builder output. Whether you keep the K+ ions from the charmm builder or add in your own with leap, you just need the correct amount to charge neutralise the protein ... as I said you may also wish to add additional salt ions.
All the best,
Callum
________________________________________
From: Fabian gmail <fabian.glaser.gmail.com>
Sent: Monday, March 28, 2016 7:15 AM
To: AMBER Mailing List
Subject: [AMBER] membrane protein complex preparation
Hi,
I am preparing a membrane-protein system for running and I have several questions:
I am still puzzled by the right way to neutralize membranes. Is it necessary to neutralise the membrane at all? Or only the protein
The only way I found to work properly is the following, is this a good strategy?
I got the DOPC_128.pdb file from applying charmmlipid2amber.py to the output of CHARM GUI. The question is should I keep the K+ atoms from this DOPC_128.pdb file? Or should I recharge using the following procedure?
Will this procedure keep intact the membrane structure? (despite the splitting warnings)?
Is this necessary or I just join the PDB files after preparing the protein only with propka for example and do not try to neutralize the membrane?
Here is the method I am trying to use:
tleap
source leaprc.lipid14
source leaprc.ff12SB
loadamberparams frcmod.ionsjc_tip3p
mem = loadpdb DOPC_128_membrane.pdb
pep = loadpdb DOPC_128_protein.pdb
addions pep Na+ 0 #that adds Na+ to the protein
addions2 mem Cl- 0 #this adds Cl- for neutralizing the membrane
complex = combine { mem pep } #will this destroy the membrane organization?
translate complex { 0 0 20 } #moves the system up to make it assymetric
set complex box { 101 101 110 } #adds length on Z for the water
solvateBox complex TIP3PBOX 0.1 # avoid adding water on the X Y directions
saveAmberParm pep complex.prmtop complex.inpcrd
savepdb complex complex.pdb
Thanks a lot,
Fabian
Fabian Glaser
Head of the Structural Bioinformatics section
Bioinformatics Knowledge Unit - BKU
The Lorry I. Lokey Interdisciplinary Center for Life Sciences and Engineering
Technion - Israel Institute of Technology, Haifa 32000, ISRAEL
fglaser at technion dot ac dot il
Tel: +972 4 8293701
http://bku.technion.ac.il
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Mar 28 2016 - 07:00:04 PDT
