Check the program Biomer. I allows you to create any type of DNA
molecule: http://casegroup.rutgers.edu/Biomer/index.html
You will also need the amber forcefield for DNA.
Gerrit
Message: 7
Date: Fri, 10 Apr 2009 12:21:33 +0800
From: li ming <mingli1...@gmail.com>
Subject: Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
To: Discussion list for GROMACS users <gmx-users@gromacs.org>
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<114aa2a90904092121m58c2eceaq42ce8731c9aa...@mail.gmail.com>
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Hi, Mark:
I want to check the chain length of DNA on the translocation time
through a
nanopore. So the DNA chains with different polymerization but the same
monomer structure is necessary. How can I solve this problem?
Does anybody has a optimized DNA pdb file for GMX simulation?
Thanks a lot!!
Ming
2009/4/10 Mark Abraham <mark.abra...@anu.edu.au>
li ming wrote:
Hi, all...
I have a question on the pdb files of DNA:
How can I obtain an appropriate DNA pdb file for GMX simulation? I
just
download some pdb files from Internet, but it is not compatible
for GMX,
saying that the residue was not found in rtp file. How can I solve
this
problem? Are the references available on this problem?
Perhaps you should start by searching for some tutorial material with
emphasis on these types of simulation.
Furthermore, if I want to get several DNA pdb files with increasing
degree
of polymerization (such as 10, 20, 50 etc.). How can I achieve
this goal?
This may or may not be easy to achieve, but you should start by
describing
it more fully. What are you wanting to polymerize, and what do you
mean by
that word?
Mark
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--
Ming Li
Institute of Chemistry,Chinese Academy of Sciences
Zhongguancun, Beijing, 100080, P. R. China
Tel: +86-10-13811601014 / 62564829
E-mail: lim...@iccas.ac.cn / mingli1...@gmail.com
...........................................................................................
Knowledge is a city to the building of which every human being
brought a
stone.
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Gerrit Groenhof
MPI biophysical chemistry
Goettingen
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http://wwwuser.gwdg.de/~ggroenh/
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