From: Branko (bdrakuli_at_chem.bg.ac.rs)
Date: Mon Nov 02 2015 - 16:26:57 CST
I didn't sue Deca-alanine tutorial, but from:
it is very obvious that pdb and psf files are already included in
tutorial; maybe you just should to download all tutorial files
-------- Original Message --------
Subject: Re: namd-l: about deca alanine tutorial setup
Date: Mon, 2 Nov 2015 23:14:28 +0100
From: Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
Reply-To: namd-l_at_ks.uiuc.edu, Ajasja Ljubetič <ajasja.ljubetic_at_gmail.com>
To: namd-l <namd-l_at_ks.uiuc.edu>, Jessen Lucas <jessenlucas0_at_gmail.com>
You can use VMD's Molefacture plugin
particular the build->protein builder).
I also have good experience with chimera
All the best,
On 2 November 2015 at 22:22, Jessen Lucas <jessenlucas0_at_gmail.com
Dear NAMD users,
I was reading NAMD Stretching Deca-alanine Tutorial
and I was curious about how to generate 10 ALA pdb and psf and par
files, it gives directly. and in my opinion, at least I should have
pdb file of 10 ALA, but how I could get that? I could not find 10ALA
in PDB website.
And also I found that if I use CHAMm to generate 10 ala, the 104
atoms is different with 104 atoms provided in NAMD tutorial (maybe
last 9 atoms are different).
Could anybody help me? is there any setup file and pdb file?
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