Messages

1

MD simulations / Re: analysis of new bases

« on: May 06, 2015, 06:37:16 am »

  Oh I am sorry for not providing a pdb sample before.
  So below is a sample. The the names of the atoms of the outer ring of new bases(residue11 and residue32) are changed to typical DA and DT(for example residue 11 has a N1 C2 N3 C4 C5 C6 ring, and residue 32 has a N1 C2 N3 C4 C5 C6 ring).
  But 3dna package even cannot recognize residue 11as a base.
  Thanks.

2

MD simulations / Re: analysis of new bases

« on: May 05, 2015, 03:43:27 am »

  Thanks for the previous instruction！
  But after changing the name of the atoms of outer ring of my  base to "N1,C2,N3,C4,C5,C6"(eventhough the atom is not a N atom, i just give it a name of N1) it also said that "non-base:residueDA11 on chain".
  I thought maybe the order of the atoms or sth. else caused the wrong.
  So are there something else for base recognizing in our package？(since i cannot find how it recognize bases in the article published before.)

3

MD simulations / Re: analysis of new bases

« on: April 20, 2015, 07:23:47 am »

Here is one of my pdf file in the trajectory to analyze.
The residue labled 11 and 32 are the two new bases(i have changed its name to normal ones).
And the origional structure of the one unnatural bases is listed below.
When conducting the 'analyze', it says 'Non-base: residue DA 11 on chain [#11]'.

4

MD simulations / analysis of new bases

« on: April 17, 2015, 09:17:48 am »

i used 'analyze' to analyze the trajectory of my DNA molecule.
maybe because a base pair differs from the natural ones too greatly, it says that this site has no residue.(i have changed the name of the new bases in the pdb file to normal one like a 'C')
HOW can i solve it？