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
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Received on Mon Mar 28 2016 - 04:30:04 PDT
