3DNA Forum

Questions and answers => MD simulations => Topic started by: sryatpku on April 17, 2015, 09:17:48 am

Title: analysis of new bases
Post by: sryatpku 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？
Title: Re: analysis of new bases
Post by: xiangjun on April 17, 2015, 09:41:02 am: Please provide a concrete example so others can reproduce the problem.

Thanks,

Xiang-Jun
Title: Re: analysis of new bases
Post by: sryatpku 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]'.
Title: Re: analysis of new bases
Post by: xiangjun on April 20, 2015, 11:57:28 pm: Thanks for providing a sample PDB datafile that helps show the problem. According to the PDB file, residues 11 and 32 have the atomic names shown in the attached images. Neither of them contains a pyrimidine ring with base atoms labeled (N1, C2, N3, C4, C5, C6). Therefore, they are not recognized as bases by 3DNA and DSSR.

Simply changing residue names (e.g., to DA) does not work -- 3DNA/DSSR uses an geometric approach to automatically detect nucleotides that does not rely on residue names. See also my post "Weird atom names of ligand thiamine pyrophosphate (TPP) (http://x3dna.org/articles/weird-atom-names-of-ligand-thiamine-pyrophosphate-tpp)". More details of the underlying algorithm is described in the coming DSSR paper. Given the above information, you can play around with names of base atoms if you really want to trick 3DNA/DSSR into taking residues 11 and 32 as nucleotides.

HTH,

Xiang-Jun
Title: Re: analysis of new bases
Post by: sryatpku 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.)
Title: Re: analysis of new bases
Post by: xiangjun on May 05, 2015, 07:27:58 am: Attaching the file with your modified names would help to show why it did not work.

Xiang-Jun
Title: Re: analysis of new bases
Post by: sryatpku 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.
Title: Re: analysis of new bases
Post by: xiangjun on May 07, 2015, 11:37:49 am: Thanks for providing an example file to illustrate the problems you have. Please always do so in the future -- this will help avoid misunderstandings and get your problems solved quicker.

You changed atom names for the modified bases to N1, C2 ... C6 as suggested, and that's good (see attached image). The issue is that your residues 11 is quite far off the default cutoff of recognized nucleotides. If you add option '-ntcutoff=0.45' (or an even higher value), residue 11 will be recognized as a nucleotide, as you would expert. See another recent thread "3DNA changes base-pair order (http://forum.x3dna.org/md-simulations/3dna-changes-base-pair-order/)". As for residue 32, you now have two N1 atoms in the same residue (see attached image). Is that intended?

HTH,

Xiang-Jun