Problems with Ruby MD and Creating ssRNA

[HenryFisher]

Hi Xiang-Jun

In reply to your answer to my initial question, viewtopic.php?f=11&t=195&start=15, I have tried the steps that you suggested.  I have added the .exe to line #425 of 'x3dna_md.rb'.  I then executed:

Code: [Select]

x3dna_md.rb -b bpfile.dat -e sample_md0.pdb and I think this now works.  Thanks  

With regards to using 'fiber', I have managed to make an ssDNA molecule but cannot work out how to form an ssRNA as it won't accept any 'Us' in my sequence.  I have tried:

Code: [Select]

fiber -a, -20 rna.pdb however this just returns the help file so I assume I've entered it wrong.

Also, Is it possible to give ssRNA molecules any secondary structures such as stem loops?

Thanks
Henry

[HenryFisher]

OK I have just worked out how to make ssRNA molecules by following FAQ#6.  Although after carrying out

Code: [Select]

pdb_frag A 1:18 name.pdb ssname.pdb it removes the bond between 5' phosphate and the 3' OH between all the nucleotides, why has this happened and also can I fix it?

Although I am still wondering about the secondary structures, I have a number of RNA sequences (18' to 21' mers) all of which have different secondary structures according to QuickFold (http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold) and am just interested to know whether it is possible with x3dna.

Thanks very much for your help with this very useful programme

Henry

[xiangjun]

it removes the bond between 5' phosphate and the 3' OH between all the nucleotides, why has this happened and also can I fix it?

I do not get it. Please be specific, using a concrete example to illustrate your problem.

Although I am still wondering about the secondary structures, I have a number of RNA sequences (18' to 21' mers) all of which have different secondary structures according to QuickFold (http://mfold.rna.albany.edu/?q=DINAMelt/Quickfold) and am just interested to know whether it is possible with x3dna.

3DNA do not predict RNA secondary structures -- there are quite a few existing methods out there already. Given a 2nd structure, I am not aware of an automatic way to convert it into 3-dimensional coordinates; 3DNA certainly does not have such functionality. In the current issue of Nucleic Acids Research (Volume39, Issue10), there is an article titled "ModeRNA: a tool for comparative modeling of RNA 3D structure" for  comparative modeling of 3D RNA structures. You may find useful information in it.

I do believe 3DNA has the facilities/potential for RNA 3D structure modeling. If you provide details as to what you want to achieve, what you've tried and the problems you still have, I may be able to help in a more concrete way.

Xiang-Jun

[HenryFisher]

The problem that I encountered was that described here http://3dna.rutgers.edu/x3dna/faqs#backbone under FAQ #6.  

The RMSD between all atoms in the original bdl084.pdb file and the generated bdl084_3dna.pdb file is only 0.73 Å. Please note that in the rebuilt bdl084_3dna.pdb file, some O3'(i-1) to P(i) linkages can be quite long (broken).

I managed to fix this however by editing the bp_step.par file directly from:

10 # base-pairs
   0 # ***local base-pair & step parameters***
#      Shear  Stretch  Stagger Buckle Prop-Tw Opening   Shift  Slide    Rise    Tilt    Roll   Twist
[red:3hxnsdr9]T-A[/red:3hxnsdr9]  -0.03   -0.10    0.09    0.04  -15.13   -1.88    0.00    0.00    0.00    0.00    0.00    0.00
[red:3hxnsdr9]T-A[/red:3hxnsdr9]  -0.03   -0.10    0.09    0.04  -15.13   -1.88    0.01    0.45    3.36   -0.00    1.71   35.97
...

to:

10 # base-pairs
   0 # ***local base-pair & step parameters***
#      Shear  Stretch  Stagger Buckle Prop-Tw Opening   Shift  Slide    Rise    Tilt    Roll   Twist
[red:3hxnsdr9]U[/red:3hxnsdr9]  -0.03   -0.10    0.09    0.04  -15.13   -1.88    0.00    0.00    0.00    0.00    0.00    0.00
[red:3hxnsdr9]U[/red:3hxnsdr9]  -0.03   -0.10    0.09    0.04  -15.13   -1.88    0.01    0.45    3.36   -0.00    1.71   35.97
...

before using the rebuild command.  This seems to have worked perfectly for all of my RNA molecules.  

With regard to the secondary structure of the molecules, thanks very much for the link to the Rother et al' article, I'm sure this will be very useful.  My goals at the moment for 3D structure modelling is to 1) have a 3D model of predicted secondary structure of RNAs (18' to 21' mers) in solution (across a range of solution conditions ideally) and 2) to have a 3D model of predicted structure as a negative gas phase ion (including predicting which phosphate groups are protonated and which hold negative charge).

Thanks Very much for your help and prompt replys

Henry