Basic Minimization Script

Please read the Basic Input Script section if you have had no prior experience in creating a basic CHARMM input script.

Preparation
This tutorial for making a basic minimization input script continues from the Basic Input Script tutorial. The protein with the PDB.org ID of 1YJP will be used in this part of the tutorial. The PDB file and an associated water box are available from the main tutorial web site http://www.charmmtutorial.org/http://www.charmmtutorial.org. should have been combined into a single structure before minimization is attempted.

Create an input script, reading in the RTF and Parameter files. After this is done, the user must read in the appended PSF and CRD files that were created by the basic input script. This can be done with the following commands:

CHARMM has the ability to work with and compare different coordinate sets. this tutorial, the root mean squared (RMS) difference between the structure before and after minimization will be computed. it is necessary to store the initial coordinates by copying them to the comparison set. "COOR" signifies that the user will retrieve the coordinates and "COPY" tells CHARMM what the users intent is with the coordinates. "COMP" is short for comparison set, so CHARMM knows the user wants to copy the coordinates to the comparison set. The line should look like:

SHAKe and non-bonded parameters
It is a good idea to fix hydrogen bond lengths in place to remove high frequency motion from the system, allowing the use of 1 fs time steps. can be accomplished with the "SHAKe BONH PARAmeters" command.

It is also necessary to set the non-bonded parameters to the same values that will be used for dynamics. full discussion of these parameters is given in the dynamics section.

Applying minimization
To tell CHARMM that a minimization is requested, start the command with "MINI". Next, choose what algorithm to use. This tutorial will first use steepest descent since for many structures it is likely to provide a substantial energy loss in a relatively short period of time. To inform CHARMM of this decision follow "MINI" with "SD". specify the number of steps, the "NSTEp" option is used followed by the number of steps. The line should look like the following:

To use the ABNR algorithm, do the same thing as above except replace "SD" with "ABNR". The number of steps can be set to 100 the same way it was for steepest descent. CHARMM can print a report on minimization so with every set number of steps, CHARMM will print a notice in the output file. This can be done with the "NPRInt" command followed by the interval in which a notice should get printed.

With ABNR, minimization can end early if the root mean square of the gradient (GRMS) reaches a certain number. The smaller the number it is, the longer the minimization will run (unless it is terminated early by "NSTEp"), however a larger number will result in a less precise minimization. For this tutorial, the relatively large tolerance of 0.05 is used. the number of print intervals, use the command "TOLGrad" followed by "0.05". The next line should now look like:

To compare the RMS value to one previous to minimization, use the line:

CHARMM will print the RMS between the main coordinate set (which now contains the minimized structure) and the comparison set (which still has the original coordinates).

To end the minimization process, write out a PDB file containing the new minimized structure, and then terminate the CHARMM script.

The final input file should resemble the following:

* Minimize PDB
*
bomlev -2

! Read in Topology and  Parameter files
OPEN UNIT 1 CARD READ NAME top_all27_prot_na.rtf
READ RTF CARD UNIT 1
CLOSE UNIT 1

OPEN UNIT 1 CARD READ NAME par_all27_prot_na.prm
READ PARA CARD UNIT 1
CLOSE UNIT 1

! Read sequence from the PDB coordinate file
OPEN READ UNIT 27 CARD NAME 1yjp-full.psf
READ PSF CARD UNIT 27
CLOSE UNIT 27

OPEN READ UNIT 10 CARD NAME 1yjp-full.crd
READ COOR CARD UNIT 10
CLOSE UNIT 10

! constrain hydrogen bond lengths with SHAKe
SHAKe BONH PARAmeters 

! non-bond setup (same values as will be used in dynamics)
NBONd INBFrq -1 ELEC FSWItch VDW VSWItch CUTNb 16. CTOFnb 12. - 
  CTONnb 8. 

ENERgy

COOR COPY COMP
MINI SD NSTEp 100
MINI ABNR NSTEp 1000 NPRInt 100 TOLG 0.05
COOR RMS

OPEN WRITE UNIT 1 CARD NAME 1yjp-full-min.pdb
WRITE COOR PDB UNIT 1
* new_1yjp-11213-min.pdb
*

OPEN WRITE UNIT 1 CARD NAME 1yjp-full-min.crd
WRITE COOR CARD UNIT 1
* new_1yjp-11213-min.crd
*

STOP