3DNA Forum

Questions and answers => MD simulations => Topic started by: souviksur on April 07, 2012, 03:35:08 am

Netiquette · Download · News · Gallery · Homepage · DSSR Manual · G-quadruplexes · DSSR-Jmol · DSSR-PyMOL · DSSR Licensing · Video Overview· RNA Covers

Title: Analysis of PDB file
Post by: souviksur on April 07, 2012, 03:35:08 am

Hello Every one,

I tried to run "manalyze" using my pdb, but it was running, can you please suggest is there any problem in my pdb file, and I also want to generate the .out file. Please suggest me, I am attaching the pdb file.

regards & thanks,
SOUVIK

Title: Re: Analysis of PDB file
Post by: xiangjun on April 07, 2012, 09:21:16 am

Hi,

The simple Perl script manalyze was introduced around v1.5 for the analysis of "multiple" structures. Over the years, I've not been aware of its usage: your question is the first one. As of v2.1beta, I am migrating from Perl to Ruby as the scripting language for 3DNA. Now manalyze and most other not widely used Perl scripts are moved out the $X3DNA/bin/ directory into $X3DNA/perl_scripts/ -- they are obsolete, but kept there for the record.

As of 3DNA v2.1, the Ruby script "x3dna_ensemble" should be used for the analysis of NMR ensembles or MD simulation trajectories. Type -h for detailed info, and run the examples to get familiar with its usage/functionality.

Your attached PDB file contains only one model, so you can use the find_pair/analyze combination to calculate 3DNA parameters. Note, however, your structure has poor geometry, as shown in the image below. As a rule, one should always perform "sanity" check to ensure sensible results.

HTH,

Xiang-Jun

Created and maintained by Dr. Xiang-Jun Lu [律祥俊] (xiangjun@x3dna.org)
The Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.