Re: [AMBER-Developers] Missing/Different files in Tutorial A3

From: Jason Swails <>
Date: Fri, 22 Jul 2011 15:25:48 -0400

I'll check for broken links and add any missing files.


Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
On Jul 22, 2011, at 3:06 PM, MengJuei Hsieh <> wrote:
> Hi,
> A undergrad project student in our lab reports that she can't find ras.pdb
> and raf.pdb from the website. Although ras.pdb can be found at python
> tutorial, raf.pdb is nowhere to be found. I thought it might be worthwhile
> to mention that tutorial takers can use a text editor to copy the first part
> of the PDB from ras-raf.pdb as ras.pdb and second part as raf.pdb,
> respectively. However then I see a potential problem for this, there is a
> magnesium ion in the end of ras-raf.pdb but not in the ras-raf.prmtop file.
> So I guess we need to modify the ras-raf.pdb as well.
> I can add a small section into the document if you guys think it's okay to
> directly modify it. :p
> Best,
> -- 
> Mengjuei Hsieh, Molecular Biology & Biochem, Univ. of California Irvine.
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Received on Fri Jul 22 2011 - 12:30:03 PDT
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