From: Mert Gür (gurmert_at_gmail.com)
Date: Wed Dec 05 2007 - 09:04:57 CST
Thanks a lot to you all .I think it worked.
Mert
On 12/2/07, Peter Freddolino <petefred_at_ks.uiuc.edu> wrote:
>
> 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------=_Part_1677_20620467.1196867097395--
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