Re: how to perform MD with two proteins

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Sun Dec 02 2007 - 10:31:54 CST

It's also possible to do this in one psfgen run. You do, however, need
to have one pdb file for each peptide; at that point, you can do
something like the following. Here I'm assuming that your files are
named a.pdb and b.pdb.

topology top_all22_prot_na.inp ;# or whatever you prefer

segment A {
    pdb a.pdb
    first NTER
    last CTER
}

coordpdb a.pdb A

segment B{
    pdb b.pdb
    first NTER
    last CTER
}

guesscoord

writepsf combined.psf
writepdb combined.pdb

Peter

Richard Wood wrote:
> Hi Mert,
>
> You need to generate a separate psf for each peptide, and then combine
> the two psf files into one single psf. It might be best (and easier?)
> to use psfgen that comes with NAMD to do that(?). I've not used VMD
> to generate psf files, but I have used psfgen on ligand protein
> complexes, and I had to generate a psf for each part, and then combine
> them into one psf (and pdb) file.
>
> HTH.
> Richard
>
> Richard L. Wood, Ph. D.
> University of Minnesota
> Dept. of Medicinal Chemistry,
> College of Pharmacy
> 717 Delaware St. SE
> Minneapolis, MN 55419-2959
> rwoodphd_at_yahoo.com
>
>
> ----- Original Message ----
> From: Mert Gür <gurmert_at_gmail.com>
> To: namd-l_at_ks.uiuc.edu
> Sent: Sunday, December 2, 2007 8:35:14 AM
> Subject: namd-l: how to perform MD with two proteins
>
> Hi,
> I have generated two simple peptides in hyperchem and merged them here
> to an single pdb.
> peptide 1: asn asp met phe arg leu
> peptide 2: leu leu phe met gln his
> As I am generating the psf file in VMD as given in the tutorial the
> second peptide is destroyed.
> Can anybody help me with that problem.
> Or if you have advices how to model this two peptides in NAMD that
> would help also.
> Thanks in advance
> Mert Gür
> Koc University/Istanbul
>
>
> bunlarin uclarini cap et, ve su icinde birbirlerine parallel sekilde,
> herbiri birer beta strand seklinde, asn ile leu uclari birbirinin
> karsisina gelecek sekilde paralel olarak yerlestir. bu durumda leu ile
> his uclari da karsi karsiya olacak.
>
> uzunca bir molekuler dinamik trajectorysi yap. baslarda bu ikisinin
> birbirine yaklasacagini ve ve bind edeceklerini dusunuyorum. zaman
> icinde bind edip etmediklerini izleyebilirsin.
>
> bind ettiklerinden emin olduktan sonra uzun bir md trajectorysi elde et.
>
> bu hesaplari protein peptide binding calismasina bir on hazirlik
> olarak yapiyor olacaksin. bind etmis olan iki peptide'in fluctuation
> correlationlarini incelemete yarar var. yaptigin her islemi yaptigin
> anda bana email ile bildirirsen, bunlari senin doktora dosyana
> koyacagim ve calismalarinin hangi asamada oldugunu izleyebiliyor
> olacagim.
>
>
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