Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
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 Subject: Re: [gmx-users] How to obtain a approperiate PDB file of DNA? To: Discussion list for GROMACS users Message-ID: <114aa2a90904092121m58c2eceaq42ce8731c9aa...@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!! Ming 2009/4/10 Mark Abraham 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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- 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. -- next part -- An HTML attachment was scrubbed... URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20090410/937f6a4a/attachment.html -- ___ gmx-users mailing list gmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! End of gmx-users Digest, Vol 60, Issue 65 * -- Gerrit Groenhof MPI biophysical chemistry Goettingen Germany http://wwwuser.gwdg.de/~ggroenh/ ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
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 > 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 > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please search the archive at http://www.gromacs.org/search before posting! > Please don't post (un)subscribe requests to the list. Use the www interface > or send it to gmx-users-requ...@gromacs.org. > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- 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. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] How to obtain a approperiate PDB file of DNA?
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 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
