Recent Posts

91

MD simulations / Re: generate DNA pdb file for Gromacs

« Last post by dnalectronics on October 27, 2021, 01:00:46 pm »

Would you mind explaining to me how did you generate pdb file for your DNA sequence. I am new to this and stuck now on creating pdb file for my MD simulation. I will appreciate any kind of help here.

92

MD simulations / DNA step parameters

« Last post by dnalectronics on October 27, 2021, 09:18:45 am »

I am an experimentalist working on DNA-drug binding. However, to support my result I am trying to do simulation. Since I don't have an experimentally determined structure for my custom 12-mer DNA duplex, I have to create one from scratch. I am using  w3dna.rutgers.edu,  to create a wide variety of nucleic acid structures.  However, I want to know what is base parameter file or where can I get that file.

I will really appreciate if you can please guide me.

Thank you for your help.

93

RNA structures (DSSR) / Re: dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by xiangjun on October 22, 2021, 05:07:20 pm »

As mentioned in my previous response, DSSR Pro has options to handle such cases, among other features.

DSSR Pro's default output reports 146 nucleotides, along with a diagnostic note for the two deformed bases. Such deformed bases can participate in a variety of loops but not in pairing interactions.

Processing file '6nd42.pdb'
  2.G.248 0.808 -- distorted, without fitted base frame
  2.G.323 0.319 -- distorted, without fitted base frame
    total number of nucleotides: 146

DSSR Pro also has an option that treats those distorted bases as normal for base-pairing interactions.

94

RNA structures (DSSR) / Re: dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by zcx on October 22, 2021, 02:40:45 pm »

This is probably misleading. For the sake of calculating base pairs, I completely agree that we should not consider nucleobases with highly distorted conformation. However, when counting how many nucleotides are there in the sequence (e.g., when generating ct or dbn files), nucleotides with distorted base conformation (or even nucleotides without their base groups) are still nucleotides. It may not be a good idea to just delete them from the sequence without at least printing out a warning message.

95

RNA structures (DSSR) / Re: dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by xiangjun on October 21, 2021, 09:47:35 pm »

DSSR is behaving as designed. Please see the section "Identification of nucleotides" of  the 2015 DSSR paper:

A nucleotide is identified if a residue contains at least three base ring atoms and the root-mean-square deviation (rmsd) of the fit falls below a user-definable cutoff. Since base rings are rigid, the rmsd is normally <0.1 Å. To account for experimental error and special non-planar cases, such as 5,6-dihydrouridine (H2U) in yeast tRNA^Phe (Figure 2), the default rmsd cutoff is set to 0.28 Å.

The default DSSR cutoff values are based on extensive tests in real-world applications. Any unidentified nucleotide is almost always due to heavy distortions in its base geometry that is 'beyond recognition'. For example, G248 in your attached 6nd42.pdb file has the PyMOL rendered image as attached. Note the N1-C2 distance is 2.2 Å, far larger than ~1.5 Å (the normal covalent C-N bond length).

DSSR Pro has provisions to handle extreme cases like yours.

96

RNA structures (DSSR) / dssr did not recognize some canonical nucleotide in 6nd4 chain 2

« Last post by zcx on October 21, 2021, 07:52:52 pm »

I am using dssr version v1.9.10-2020apr23 to analyze PDB 6nd4 chain 2. There are 146 standard nucleotides in this chain. However, when I run

x3dna-dssr -i=6nd42.pdb  -o=output.dssr

It reports
    total number of nucleotides: 144

This also causes the dssr-2ndstrs.dbn files to have 144 rather than 146 positions. It seems dssr disregard residue G248 for unknown reason.

97

RNA structures (DSSR) / Re: DSSR output

« Last post by xiangjun on October 07, 2021, 09:47:56 am »

Which version of DSSR are you using?

98

RNA structures (DSSR) / DSSR output

« Last post by kirkpacc on October 07, 2021, 06:54:00 am »

I am running DSSR from within a python program using os.system().  It works well, but I would like to suppress all of the screen output.  I can redirect the screen output, but would prefer that it did not happen at all.  Is there an option to set to do this?

99

w3DNA -- web interface to 3DNA / Re: why w3DNA fails to calculate some non-canonical base pairs in structure

« Last post by xiangjun on September 16, 2021, 11:30:57 am »

Hi Ying,

Given the information you provided, I can only conclude that there must be some oddity in your structure at the places where 3DNA is unable to detect the base pairs. I cannot provide any further advice before seeing the structure (or the relevant section of it).

Xiang-Jun

100

w3DNA -- web interface to 3DNA / Re: why w3DNA fails to calculate some non-canonical base pairs in structure

« Last post by Ying on September 16, 2021, 10:21:36 am »

Dear Xiang-Jun,

Attached please find the part of analysis done via w3DNA for my PDB, and I found that the analysis just escape 4 adenosines for all types of calculation. The sequence (5'---3') is GGGC(CAG)5GUCC. Thank you very much for your help.

Best wishes,

Ying