Energy minimization of a protein with NAMD

 

1 Introduction
2 What's you need
3 NAMD installation
4 Protein download
5 Protein preparation
6 Creation of the input files for NAMD
7 Run the NAMD calculation
8 Analysis of the results
9 Using the atom constraints
    9.1 Atom fixing
    9.2 Atom constraints

 

1 Introduction

VEGA ZZ allows to prepare the input files for NAMD in easy way without the use of complex softwares to generate the topology. In this tutorial is explained step-by-step how to perform a simple conjugate gradients energy minimization of the crambin crystallographic structure with and without constraints.

 

2 What's you need

 

3 NAMD installation

 

4. Protein download

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

 

5 Protein preparation

 

6 Creation of the input files for NAMD

NAMD requires several files: the PDB and the PSF file of the molecule, one or more parameter files and a command file defining the condition of the calculation.

numsteps                10000
minimization            on
dielectric              1.0
coordinates             1CRN.pdb
outputname              1CRN
outputEnergies          1000
binaryoutput            no
DCDFreq                 1000
restartFreq             1000
structure               1CRN.psf
paraTypeCharmm          on
parameters              par_all22_prot.inp
parameters              par_all22_vega.inp
exclude                 scaled1-4
1-4scaling              1.0
switching               on
switchdist              8.0
cutoff                  12.0
pairlistdist            13.5
margin                  0.0
stepspercycle           20

Save the file with the 1CRN_min.namd name. This file allows to perform a 10000 steps conjugate gradients minimization, saving the output (coordinates and restart files) every 1000 iterations. For more information about the parameters, please consult the NAMD User Guide.

 

7 Run the NAMD calculation

namd2 1CRN_min.namd

and hit return. If you want to save the output in a file, use this command:

namd2 1CRN_min.namd > 1CRN.out

If you have more than one CPU installed, you can speed-up  the calculation specifying the total number of CPUs:

namd2 +p2 1CRN_min.namd > 1CRN.out

In this case the PC has two CPUs and both are used for the calculation (+p2 option). The dual core (e.g. Athlon X2, Pentium D, Core 2 Duo, etc) and the Pentium 4 with hyperthreading should use the +p2 option.

 

8 Analysis of the results

The calculation results are contained mainly in two files: the 1CRN.dcd (trajectory file) and the 1CRN.out, if you saved it. The first one is a binary file and can't be opened with a text editor. It contains the atom coordinates of each saved frames (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.

 

9. 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.

 

9.1 Atom fixing

numsteps                10000
minimization            on
dielectric              1.0
coordinates             1CRN_fix.pdb
outputname              1CRN_fix
outputEnergies          1000
binaryoutput            no
DCDFreq                 1000
restartFreq             1000
structure               1CRN.psf
paraTypeCharmm          on
parameters              par_all22_prot.inp
parameters              par_all22_vega.inp
exclude                 scaled1-4
1-4scaling              1.0
switching               on
switchdist              8.0
cutoff                  12.0
pairlistdist            13.5
margin                  0.0
stepspercycle           20
fixedAtoms		on
fixedAtomsCol		B

In red are indicated the differences with the standard minimization file. Please note that the PSF file is the same of the previous minimization because the molecule isn't changed.
Save the file with 1CRN_fix_min.namd file name.

namd2 1CRN_fix_min.namd > 1CRN_fix.out

 

9.2 Atom constraints

numsteps                10000
minimization            on
dielectric              1.0
coordinates             1CRN_const.pdb
outputname              1CRN_const
outputEnergies          1000
binaryoutput            no
DCDFreq                 1000
restartFreq             1000
structure               1CRN.psf
paraTypeCharmm          on
parameters              par_all22_prot.inp
parameters              par_all22_vega.inp
exclude                 scaled1-4
1-4scaling              1.0
switching               on
switchdist              8.0
cutoff                  12.0
pairlistdist            13.5
margin                  0.0
stepspercycle           20
constraints             on
consref                 1CRN_const.pdb
conskfile               1CRN_const.pdb
conskcol                B

In red are indicated the differences with the standard minimization file. Save the file with 1CRN_const_min.namd name.

namd2 1CRN_const_min.namd > 1CRN_const.out