From: Andres Morales N (andresmoralesn2_at_hotmail.com)
Date: Wed Mar 16 2011 - 14:22:09 CDT
I know the sequence of the peptide. The main problem is that I don't know how to built it. Coul I do it with VMD or any other program?
Date: Wed, 16 Mar 2011 08:54:00 -0700
Subject: Re: namd-l: Bactenecine
Do you know the sequence of this peptide? If so, couldn't you build it and then "dock" it into your membrane (or a piece of it)? That's how I placed a molecule on the surface of a membrane.
From: Andres Morales N <andresmoralesn2_at_hotmail.com>
To: VMD <vmd-l_at_ks.uiuc.edu>; NAMD <namd-l_at_ks.uiuc.edu>
Sent: Mon, March 14, 2011 11:11:05 PM
Subject: namd-l: Bactenecine
I need to simulate the interaction of the peptide (Bactenecine) with a phospholipid monolayer. So I havenít be able to find Bactenecinís crystal structure (pdb file) yet. Does anybody know where I could find it? Another option is to model that peptide since its amino-acid sequence, i.e, I need to make a pdb file of its random coil using special coordinates of its atoms (it is a 19-reside peptide). I havenít worked in this before. Could I use VMD to do it? Or is there any program to do it? I hope anybody can help me.
Andrťs Morales N.
Biophysics and Molecular Modelling Group
Escuela Politecnica Nacional, Quito-Ecuador
Ladron de Guevara E11-253.
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