Topics

1

MD simulations / Snapshots must be separated by MODEL/ENDMDL

« on: March 10, 2011, 10:50:17 am »

Dear Xiang-Jun,
I have just noticed another potential bug. Your ruby script looks only MODEL/ENDMDL pairs to separate each snapshot. Although this works for the sample trajectory pdb you use (which was created using gromacs), not every visualization/simulation package create the files same way. For example, vmd does not use MODEL to start each snapshot and it ends with END only. Some other programs use TER instead of END. May be we should start matching "ATOM     1 " assuming there is always a first atom from the simulation trajectory.

HTH,
Alpay

2

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

« on: February 23, 2011, 10:06:05 am »

Dear Xiang-Jun,

Thank you for your scripts! I just tested the sample set and they seem to work fine. I am glad you coded an -all option. I personally like to run these scripts once and have all the information available at the same time. In addition, this is very similar to what Curves does as well. Next step would be to incorporate some distribution calculation.

I have one small comment. Instead of printing out model_1, model_2, etc.. We should just have the snapshot numbers, since an MD trajectory tends to have thousands of them.

I look forward to using these scripts in my analysis.

Cheers!
Alpay

3

MD simulations / A modified 3DNA parser for MD trajectory analysis

« on: January 07, 2011, 06:50:10 pm »

I am attaching a python script that my be of use for trajectory analysis. I based this Python script on the code of Yurong's X3DNA parser.

Recipe:
First run nmr_strs program on your trajectory (save trajectory as one pdb file)
The python program parses the .out files generated by nmr_strs
>  nmr_strs --pdbfile test.pdb
> csh mv.txt
     script to rename files:
     you will need to rename the *.out files to "file.NUM.out" where NUM is the snapshot number from nmr_strs output.
        Example:
     mv testNUM.out test.NUM.out
     where NUM is the snapshot number.

> python parse_3dna_out.py file NUMofSNAPSHOTS NUMofBP
> python parse_3dna_out.py test 20 12
usage is: python parse3dna.py file NUMofSNAPSHOTS NUMofBP
The test file contains 100 ps snapshots from a 2 nanosecond simulation trajectory of a DNA hairpin. (20 snapshots)
NUMofSNAPSHOTS is the total number of snapshots read in nmr_strs program
NUMofBP is the number of base pairs identified for the trajectory.

This will create csv files along the trajectory for each base pair (as columns excluding the end base pair where the values are 0 or not calculated)

You can open csv files with excel or any other program.

Hope this helps,
Alpay

4

General discussions (Q&As) / triplex building

« on: September 01, 2010, 05:23:15 pm »

Hello everyone!

I am trying to build a triplex DNA structure in the form of (PPY) Purine-Purine-Pyrimidine (i.e. GGC and AAT with GC and AT Watson-crick and GG and AA Hoogsten base pairs) repeats.
The fiber option in 3DNA gives YYP triplexes. I am willing  to construct new parameter files. I just need to know how to go about it. What kind of files do i need to create and how to integrate them with 3DNA?

Thanks

Alpay