[gmx-users] -ter option of pdb2gmx

[Valentin Gogonea]

Hi gmx users,

How does the -ter option of pdb2gmx works? What do you have to specify?  
Can somebody give me an example?

Thank you for your help.

Valentin

On Thursday, March 20, 2003, at 07:04 PM, Graham Smith wrote:

>
>> now planning to insert a alpha helical peptide in the headgroup
>> region of the equilibrated bilayer. I was wondering if Drs. Lindahl,
>> Van der Spoel, I didn't want to solvate the peptide as it would
>> affect it's structure before I place ina equilibrated/hydrated
>> bilayer.
>
>> I have a similar problem with bilayers . i don't know how
>> put my peptide i=
>
>> Do either of you have any suggestions on how I could decrease the
>> potential energy of my peptide without solvating it? DMSO...could
>> that be an option??????
>
>
> Reading between the lines, I take it that you have one of those
> antimicrobial peptides (cecropins or something?) that form amphipathic
> helices with lots of lys on one side and seem to bind to lipid
> bilayers, esp. those with lots of negative phospholipid, carpeting the
> surface,  and disrupt them or make holes in them. I did a little bit
> of work on them a couple of years ago but never published anything.
>
> It seems likely that the conformation of the peptide in water will be
> different to its conformation when it is half-buried in the head-group
> region of the bilayer, and so you want to get it in the "right"
> conformation before trying to insert it. But I don't think it's
> possible to know what that conformation is until the peptide is
> inserted; then eventually it should insert itself to the depth
> where it is happiest, and its conformation should relax; but in
> practice the side chains will get tangled up with the lipid
> head groups and I would guess that it will take hundreds of ns
> for anything to happen. So this is a very hard problem.
>
> Maybe DMSO is a good idea, or any solvent with a lower dielectric
> constant than water, if you think the side chains of the peptide
> should curl up a bit rather than being extended. A low dielectric
> solvent should also help if your peptide is losing helicity in water.
> But you're still only approximating the headgropu environment.
>
> If you just want to go ahead and insert it anyway, you could use my
> gromacs-modified-to-make-a-hole thing from the contributions page
> (though I'm hesitant to suggest this after the problems some other
> people have had). You don't have to make a hole right through the
> bilayer: if you align your peptide with where you think it should be
> in the headgroups, then make a molecular surface for it, you'll be
> able (with luck) to drive the headgroups out of that volume, and so
> make a "furrow" in the surface that you could drop your peptide into.
>
> An idea that just occurs to me, if you have a nice big computer (they
> always used to at Edinburgh when I was there), is that
> you could start from a randomized mixture of lipid and water.
> Sievert-Jan Marrink did this a year or so ago and got bilayers forming
> spontanously in about 50-100 ns. If you added your peptides to
> the mixture you might find that they inhibited the formation of the
> bilayers.
>
> -Graham
>
> ####################################################################### 
> #
>
> Dr. Graham R. Smith,
> Biomolecular Modelling Laboratory,
> Cancer Research UK,
> 44 Lincoln's Inn Fields,
> London WC2A 3PX,
> U.K.
> Tel: +44-(0)20 7269 3348
> email: graham.smith at cancer.org.uk
> URL: http://www.bmm.icnet.uk/~smithgr
>
>
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