VMD-L Mailing List

From: Sebastián Gutiérrez (segumal_at_gmail.com)
Date: Wed Jul 04 2012 - 17:40:32 CDT

Vince,

Just for the record, you can also use those 35 different types of lipids
for building membrane-protein complexes.
That reduced number of lipids appear when you want to build a homogeneous
membrane.

I'm unaware of what protocol CHARMM-GUI uses to build its membranes, but it
seems to me that you can't upload your own lipid for building custom
membranes.
If i'm not mistaken, one could be able to contact CHARMM-GUI developers and
(nicely) ask them to add more lipid types. I think i read something about
it at the website, you might want to check that.
If that doesn't work, you might be able to modify VMD's membrane builder.
I'm sure that this topic has been covered in more detail in this mailing
list before.

Hope this helps!

Best regards,

Sebastián

On Tue, Jul 3, 2012 at 1:44 PM, Vince Cho <vince_at_fastmail.fm> wrote:

> Hello Sebastián,
>
> Thanks for pointing that out. Actually I just realized that too. Just to
> make things clear for other users, the number I mentioned was for building
> a protein-membrane mix.
>
> But anyway, I skimmed through all 34 lipids and still couldn't find one I
> need which has a single tail - most of these 34 lipids seemed to have
> double tails, correct me if I'm wrong.
>
> That said, do you think there's a way to utilise the protocol of
> CHARMM-GUI membrane builder for building a membrane of single-tail lipid
> molecules? I was thinking of adopting the distance between neighbouring
> lipid molecules, but I guess they might be quite different for single- and
> double-tailed lipids, no?
>
> V
>
>
>
> On 07/03/2012 11:31 AM, Sebastián Gutiérrez wrote:
>
> Hello Vince,
>
> are you sure about what you said regarding CHARMM-GUI?
> Last time i checked there were 34 different lipids available (plus
> cholesterol) for membrane building.
> Check this link:
> http://charmm-gui.org/?doc=input/membrane_only&step=1
>
> You can also build heterogeneous membranes with this tool.
>
>
> Best regards,
>
> Sebastián
>
> On Thu, Jun 28, 2012 at 12:03 AM, Vince Cho <vince_at_fastmail.fm> wrote:
>
>> Hello All,
>>
>> I have a quick question about building a membrane in general.
>> Apparently, the "membrane builder" module in VMD offers only 2 types of
>> lipid. CHARMM-GUI offers a bit more, but that's limited to 6 as well.
>>
>> So, if I want to build a membrane of an arbitrary lipid, what would be
>> the best way to proceed?
>>
>> The quick and dirty method would be to start from a PDB file of a single
>> molecule and make an array of it, but I feel like I will encounter a lot of
>> bugs this way. Is this how the Membrane Builder module works?
>>
>> Thanks,
>>
>> V
>>
>
>
>