Joseph Johnson wrote:
I can't seem to get this to work out so I think I'm giving up and asking
for some big help. I've been trying to generate a
poly(gamma-benzyl-L-glutamate) with 5 and 10 repeat units but nothing
seems to work out. Is there anyone that would be generate a pdb file
that would actually work with pdb2gmx so I could see the proper
formatting of the file?
Everyone here has their own stack of to-do's :) And besides, it's always better
to learn how to solve a problem, is it not? If formatting is a problem, see the
following:
http://www.wwpdb.org/docs.html
What exactly is the error message you're getting from pdb2gmx? You will likely
get useful help if you can demonstrate what you are doing to troubleshoot your
own problem, as I suggested here:
http://oldwww.gromacs.org/pipermail/gmx-users/2009-June/042653.html
If you've tried PRODRG, as you said in that message, I really don't know what
the problem with the PDB file would be - every structure I've obtained from the
server has had proper formatting. You can verify that for yourself at the first
link I posted.
You can also draw structures using xleap (now part of the *free* AmberTools).
There should be absolutely no problem with the formatting of those files, we've
been using them in our lab for years without ever once encountering a formatting
issue.
-Justin
I really appreciate your help, thank you :)
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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