https://github.com/haschka/pdb-nma-analysis

A tool to perform quick normal mode analysis on a PDB file using Tirion's model.
https://github.com/haschka/pdb-nma-analysis

Last synced: about 2 months ago
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A tool to perform quick normal mode analysis on a PDB file using Tirion's model.

• Host: GitHub
• URL: https://github.com/haschka/pdb-nma-analysis
• Owner: haschka
• License: gpl-3.0
• Created: 2022-07-23T01:21:01.000Z (over 2 years ago)
• Default Branch: main
• Last Pushed: 2022-10-11T09:29:53.000Z (about 2 years ago)
• Last Synced: 2023-02-28T04:01:16.775Z (almost 2 years ago)
• Language: C
• Size: 27.3 KB
• Stars: 0
• Watchers: 1
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • License: LICENSE

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README

        
# pdb-nma-analysis

(c) Thomas Haschka 2009-2022

A tool to perform quick normal mode analysis on a PDB file

according to the method first proposed by

[Tirion et al.](https://doi.org/10.1006/jmbi.1993.1135).

Please cite: [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.6888913.svg)](https://doi.org/10.5281/zenodo.6888913)

This tool now has a youtube tutorial: [https://youtu.be/jUBWMLQYkKk](https://youtu.be/jUBWMLQYkKk)

### Compiling the Program

The program was almost completely ( by exercise ) 

written using the SSE2 + SSSE3 intrinsics, and as 

such requires an intel/amd processor supporting these 

instructions to work. Anything built after 2008 basically

should do it.

The program further needs the lapack libraries. On 

a contemporary Debian Based system you should be able to obtain

all requirements using:

```

sudo apt-get install build-essential liblapack-dev

```

You can then compile the program:

```

gcc -O2 -march=native nma-double.c -o nma -lm -llapack

```

obtaining the nma binary.

### Performing Normal Mode Analysis

The nma tool is pretty self explanatory. Its arguments are:

```

file: pdb file 

   k: spring constant in atom - atom interaction potential 

 cut: Cutoff of atom - atom interaction in Angstr. 

nmax: highest mode to be visualized. nmax has to satisfy 

       7 < nmax < 100

```

in example if you download the PDB file 

[1uqq](https://files.rcsb.org/download/1QUU.pdb)

you may perform nma analysis in typing:

```

./nma 1quu.pdb pdb 0.5 15 9

```

which should yield the files:

```

7-mode.xyz

8-mode.xyz

9-mode.xyz

eigenvalues

```

The eigenvalues give you an idea of how much each

mode should get occupied as the protein gets excited.

Each mode can be visualized for instance with 

[VMD](https://www.ks.uiuc.edu/Research/vmd/)

using the Van der Waals representation

in this program you might get nice movies of each mode. 

### History

The program was in its original form written in 2009 as part of Thomas Haschka's 

Master Theses