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

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!!

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 prob