From: Richard Wood (rwoodphd_at_yahoo.com)
Date: Sun Dec 02 2007 - 10:00:43 CST
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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