[gmx-users] -ter option of pdb2gmx

[Erik Lindahl]

Hi Valentin,

You don't have to specify anything, but when you use the -ter option  
you will be asked interactively what kind of termini  
(charged/uncharged/none) you want for each chain.

Cheers,

Erik

On Thursday, Mar 27, 2003, at 12:52 US/Pacific, Valentin Gogonea wrote:

> 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
>>
>>
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-request at gromacs.org.
>>
>
------------------------------------------------------------------------ 
-----
Erik Lindahl, MSc, PhD     <lindahl at stanford.edu>
D109, Fairchild Building
Dept. Structural Biology, Stanford University School of Medicine
Tel. 650-7250754    Fax. 650-7238464

-------------- next part --------------
A non-text attachment was scrubbed...
Name: not available
Type: text/enriched
Size: 4413 bytes
Desc: not available
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20030327/eb9bb173/attachment.bin>