Energy minimization of a protein with NAMD


1. Introduction
2. What's you need
3. NAMD installation
4. Protein download
5. Protein preparation
6. NAMD minimization
7. Analysis of the results
9. Using the atom constraints
    9.1 Atom fixing
    9.2 Atom constraints


1 Introduction

VEGA ZZ allows to run NAMD calculations in easy way without the use of external software. In this tutorial, it will explained step-by-step how to perform a simple conjugate gradients energy minimization of the crambin crystallographic structure with constraints.


2 What you need


3 NAMD installation


4 Protein download

You can download the crambin (1CRN) structure by using the PDB Web interface or the tool integrated in VEGA ZZ:


5 Protein preparation


6 NAMD minimization

All input files required by NAMD are automatically generated by VEGA ZZ.


7 Analysis of the results

The calculation results are placed in the same directory in which you saved the crambin structure and the most interesting files are two: 1CRN.dcd (trajectory file) and 1CRN.out. The first one is a binary file that can't be opened by a text editor. It contains the atom coordinates of each saved frame (10 frames, because one frame every 1000 was saved). The second one is a text files containing the output messages generated by NAMD and the energy information.


8. Using the atom constraints

In order to keep the structure more close to the original crystallographic data, a common procedure is to apply atom constraints to the protein backbone. In this way, the side chains can relax themselves keeping the secondary structure. NAMD and VEGA ZZ allow to constraint the atoms in two modes: fixing the atoms or applying a force constant to the atoms restraining their movements.


8.1 Atom fixing


8.2 Atom constraints