[gmx-users] How to obtain a approperiate PDB file of DNA?

[Gerrit Groenhof]

>

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 <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>
> Message-ID:
> 	<114aa2a90904092121m58c2eceaq42ce8731c9aafef at 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.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  
>>> 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: liming at iccas.ac.cn / mingli1986 at 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
Germany
http://wwwuser.gwdg.de/~ggroenh/