Messages

1

General discussions (Q&As) / Re: Problems with Ruby MD and Creating ssRNA

« on: June 10, 2011, 05:21:49 am »

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

2

General discussions (Q&As) / Re: Problems with Ruby MD and Creating ssRNA

« on: June 09, 2011, 06:05:37 am »

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

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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

3

General discussions (Q&As) / Problems with Ruby MD and Creating ssRNA

« on: June 09, 2011, 05:36:11 am »

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:

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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:

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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

4

MD simulations / Re: Ruby scripts for the analysis of MD simulation trajector

« on: June 08, 2011, 09:20:58 am »

Since writing the above post I have followed some instructions from another post:

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export X3DNA=/usr/home/bshcf/X3DNA
export PATH=$PATH:$X3DNA/bin
chmod a+rx /usr/home/bshcf/X3DNA/bin/*
find_pair find_pair displayed the help file as expected however when using:

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x3dna_md.rb -b bpfile.dat -e sample_md0.pdb I now get another error

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3DNA settings error: can't execute C:/MinGW/msys/1.0/home/bshcf/X3DNA/bin/analyze

5

MD simulations / Issues related to 3DNA and the MD Ruby scripts set up

« on: June 08, 2011, 07:57:54 am »

Hi Xiang-Jun

I have been using x3dna recently and trying to get used to working in MinGW.  I have had some success and managed to produce a DNA molecule in a .pdb file.  However I am interested in building ssRNA molecules preferably with a theoretical secondary structure for use in AMBER MD.  I registered a couple of days ago and you recommended I use the ruby scripts for MD.  I have downloaded these scripts and extracted them to my X3DNA folder.  The first problem I encountered was when trying to run the x3dna_md.rb file with the recommended first command

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x3dna_md.rb -b bpfile.dat -e sample_md0.pdb This returned the error

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/usr/bin/env: ruby: No such file or directory  I think I fixed this by installing ruby, at least I don't get that error any more.  Now when I try to execute the command above I get

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X3DNA environmental variable not set I don't know what this means but I tried to resetting the path for X3DNA

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export X3DNA=/usr/local/X3DNA/
export PATH=$PATH:$X3DNA/bin But this didn't work.  Any help would be greatly appreciated, I hope there's enough information here, if not please let me know.  This is my first time using a Linux based command programme so I'm sorry if I've done something really stupid.

Thanks
Henry Fisher