[gmx-users] Making a .pdb file that actually works?

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 15 20:47:55 CEST 2009

Joseph Johnson wrote:
> I've tried multiple times to make a pdb file that will work with 
> pdb2gmx.  I've even drawn the molecule into PRODRG but the structure 
> will still not work.  I simply want a poly(benzyl-L-glutamate) with 5 
> repeat units.  How in the world can I get this to work?

If it is a repeat unit then you can define the constituent building blocks 
within the corresponding .rtp file.  The PDB file is not likely the problem, but 
if you want more useful help, you'll have to describe the difficulty you're 
having fully, including real error messages and snippets of the relevant 
structure and .rtp entries.


> Thank you for your time.
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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