VMD-L Mailing List

From: wolfinbm_at_uci.edu
Date: Wed Dec 27 2006 - 14:23:22 CST

Hello Peter,
Thank you very much for your help. I already have some of what you
described, thanks to Dr. Ritz and one of his graduate assistants (see
attatchments). My main problem right now (I think) is getting PETE
monomers connected together to make a polymer.

Thanks and Best,
Matt

> Hi Matt,
> you'll need to deal with two separate issues to get what you want:
> 1) creating a proper topology for the PETE polymer
> 2) getting coordinates for the membrane of interest
>
> Before getting started, you'll want to make sure you've read the namd
> tutorial (including appendices) and topology file tutorials at
> http://www.ks.uiuc.edu/Training/Tutorials/. Doing what you want to is
> still somewhat complicated; we're currently working on things like
> arbitrary polymer builders that will make it much easier. For now,
> though, you'll still have to do some things by hand, which is where the
> tutorials are useful.
>
> Dealing with these in order:
> 1. Building up pretty much any polymer using VMD/psfgen is done just
> like a polypeptide. If you look at the topology file entries for any of
> the amino acids, you'll see that bonds are specified to -C and +N --
> these denote bonds to the previous and next monomers in the polymer
> chain. You need to first generate a topology file entry for your PETE
> monomer, and then add the proper bonds to cause it to be connected in a
> chain (and also make terminal patches, like NTER and CTER, to properly
> cap the ends of your polymer). You can get the PETE monomer topology
> file using a molefacture function: In the tkcon, enter
> ::Molefacture::write_topfile pete.top $sel
> where $sel is an atomselect object containing your PETE monomer. If your
> version of molefacture doesn't have this let me know and I'll send you
> the latest alpha (which also has this command present in the file menu).
> You'll need to assign proper atom types either in molefacture or by
> editing the topology file, and then add the bonds necessary for
> polymerization. Armed with this topology file, feeding a pdb file
> containing several PETE monomers to psfgen will let you build a polymer.
>
> Since we're talking about a pdb file with the proper coordinates, this
> leads us neatly into
> 2. Getting the coordinates. You'll need to generate a pdb file
> containing the coordinates for some section of the membrane you want.
> Since I really don't know what a PETE membrane would look like, the best
> I can do is recommend the following steps:
> -Write a single pete monomer as a pdb from vmd
> -Use your favorite text editor or filter to make a pdb file with many
> copies of it, with consecutive residue numbering
> -Load that composite pdb into vmd, and use either the mouse or movement
> commands to move the residues into the appropriate places for a pete
> membrane
> -Write the new pdb file, and then run it through psfgen to get the
> polymer of interest
>
> Once you've got a single membrane layer generated, you can look at
> making several chains with different size holes punched in them to
> generate the different layers.
>
> Peter


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