The 0.15M KCl will add additional K+ and Cl- ions to your system but these are not required to charge neutralise it. You can select or deselect this option during building of the membrane in the charmm GUI.
If you have lipids placed inside the protein channel then yes, you will have to manually delete these.
Best,
Callum
________________________________________
From: Fabian gmail <fabian.glaser.gmail.com>
Sent: Monday, March 28, 2016 11:14 AM
To: AMBER Mailing List
Subject: Re: [AMBER] membrane protein complex preparation
Thanks again,
The protein charge is -7 but charmm added 14 K+….. I don’t understand why, it was with the requirement of the tutorial 0.15" M “KCl … Maybe I need to remove the K+?
Regarding the water yes, I checked and I can keep the original amber charmmlipid2amber.py
Another problem I have is that my system is a transporter in the open conformation, and then I noticed that several membrane proteins entered the transporter pathway…. How do I remove them? One by one?
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
> On 28 Mar 2016, at 6:01 PM, Dickson, Callum J <callum.dickson09.imperial.ac.uk> wrote:
>
> Hi Fabian,
>
> POPE is also charge neutral, so you should not have any charge from the membrane if it is made entirely of POPE lipid... I would think the K+ ions added are to neutralise the protein?
>
> You can load different segments of your system into xleap and calculate net charge of the unit if that helps clarify things.
>
> Correct, charmmlipid2amber.py will only convert the lipid molecules, so you'll need to delete the charmm generated protein and add back your original input protein.
>
> Cheers,
> Callum
>
> ________________________________________
> From: Fabian gmail <fabian.glaser.gmail.com>
> Sent: Monday, March 28, 2016 10:42 AM
> To: AMBER Mailing List
> Subject: Re: [AMBER] membrane protein complex preparation
>
> Dear Callum,
>
> Thanks a lot for your quick and detailed answer. I use POPE membrane, which is more charged I think, and indeed CHARMM returns 14 K+, which are there I believe to neutralise the membrane… the problem is that to prepare the protein, charmmlipid2amber.py does not work. tleap does not read its protein output, only the membrane, so I used propka for the protein only and put everything together. Now the charge command gives me the protein charge only, it obviates the membrane charge….
>
> That is the reason I am asking whith the K+ from CHARMM, and if I can trust them. If I keep the water and the K+ and add the propka processed protein, then the charge is +14 from the membrane -7 from the protein = +7, should I neutralize this charge?
>
> But this will not be addecuate I guess since the K+ are there for the membrane …. you see my confusion?
>
> 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
>
>
>> On 28 Mar 2016, at 4:52 PM, Dickson, Callum J <callum.dickson09.imperial.ac.uk> wrote:
>>
>> 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
>>
>>
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>>
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Received on Mon Mar 28 2016 - 10:00:03 PDT
