[gmx-users] How to obtain a approperiate PDB file of DNA?
ggroenh at gwdg.de
Fri Apr 10 08:52:31 CEST 2009
Check the program Biomer. I allows you to create any type of DNA
You will also need the amber forcefield for DNA.
> Message: 7
> Date: Fri, 10 Apr 2009 12:21:33 +0800
> From: li ming <mingli1986 at gmail.com>
> Subject: Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> <114aa2a90904092121m58c2eceaq42ce8731c9aafef at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
> 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!!
> 2009/4/10 Mark Abraham <Mark.Abraham at 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
>>> 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
>>> 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
>>> 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
>> it more fully. What are you wanting to polymerize, and what do you
>> mean by
>> that word?
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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: liming at iccas.ac.cn / mingli1986 at gmail.com
> Knowledge is a city to the building of which every human being
> brought a
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