Fwd: Re: about deca alanine tutorial setup

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
<http://www.ks.uiuc.edu/Research/vmd/plugins/molefacture/> (in
particular the build->protein builder).
I also have good experience with chimera
<https://www.cgl.ucsf.edu/chimera/>'s builder.

All the best,

On 2 November 2015 at 22:22, Jessen Lucas <jessenlucas0_at_gmail.com
<mailto:jessenlucas0_at_gmail.com>> wrote:

    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?

    Best regards,
    J. Lucas

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