Using GMIN to generate endpoints (CHARMM)

We can use GMIN to explore the energy landscape of our peptide and find interesting structures (endpoints) to connect using OPTIM to form a pathway. After that, we can use PATHSAMPLE to calculate the rate of interconversion of these endpoints, taking into account multiple pathways.

Setting up CGMIN

Copy the metenk.crd file you have just created into a new directory, and rename it input.crd. CGMIN expects the input to always be called 'input.crd'.

mkdir CGMIN
cp metenk.pdb CGMIN/input.crd

We now need to create a new file, data, which contains the GMIN keywords we would like to use. Copy the following into this file:

TARGET -157.082347
SLOPPYCONV 0.001
TIGHTCONV 0.00001
TRACKDATA
ACCEPTRATIO 0.3
EDIFF 0.01
DUMPINT 100
UPDATES 800
MAXIT 10000 10000
TEMPERATURE 0.8
STEPS 300 1.0
STEP 80.0 0.0
SAVE 10
CHPMAX  0.4
CHPMIN  0.2
CHNMAX  10
CHNMIN  0
CHARMMTYPE toph19_eef1_perm.inp param19_eef1_perm.inp
CHARMM
! Everything below the CHARMM line above is part of a CHARMM input file
set pardir "/home/csw34/svn/CHARMM31/toppar"

! BOMLev sets the level of warnings what do not cause the program to exit. -5 = very lax
BOMLev -5

! PRNLEV sets the ammount of output you get from CHARMM. 0 = small
PRNLEV 0

! Read standard topology and parameter files. The @top and ~par variables are set in the CHARMMTYPE line above
OPEN READ CARD UNIT 1 NAME @pardir/@top
READ RTF CARD UNIT 1
CLOSE UNIT 1

OPEN READ CARD UNIT 2 NAME @pardir/@par
READ PARAMETER CARD UNIT 2
CLOSE UNIT 2

! Generate the PSF for met-enk
READ SEQUence CARD
*
5
TYR GLY GLY PHE MET
GENErate FIRS NTER LAST CTER SETUp

! Read the initial coordinates from input.crd
OPEN UNIT 20 NAME input.crd READ CARD
READ COOR UNIT 20 CARD FREE
CLOSE UNIT 20

! Build the internal coordinate tables
IC FILL PRESERVE
IC PARAMETERS
IC PURGE
IC BUILD

! Set up the EEF1 solvent model
eef1 setup temp 298.15 unit 93 name "/home/csw34/svn/CHARMM31/toppar/solvpar.inp"
update ctonnb 7. ctofnb 9. cutnb 15. group rdie

As before, you may need to make some changes to this file, so that the paths point correctly to your CHARMM files. If you are working in CUC3 in Cambridge, this may just be as simple as changing my CRSID (csw34) for yours.

Everything above the CHARMM line is a GMIN keyword. It is highly recommended that you take a look at the GMIN documentation here, so that you know what each of them does. In brief, we are doing up to 300 basin-hopping steps (or until the TARGET - the global minimum - is found), and at each step generating new coordinates by changing between - and 10 dihedral angles (backbone or sidechain) by up to 80 degrees.

Everything below the CHARMM line is the CHARMM input that we use to set up the potential. If you'd like to know what this is doing, consult the CHARMM documentation! You may notice that is is very similar to the input we used to generate the metenk.crd file in the previous part of this tutorial.

Running CGMIN

Assuming that you have already compiled it - it's time to run CGMIN and find some minima!

CGMIN > charmm.out &