Amber Workshop - tutorial 3

(Note: These tutorials are meant to provide illustrative examples of how to use the AMBER software suite to carry out simulations that can be run on a simple workstation in a reasonable period of time. They do not necessarily provide the optimal choice of parameters or methods for the particular application area.)
Copyright Ross Walker 2004

The first thing we should do is obtain minimised structures for our two initial structures. We will then do a series of single point energy calculations on these minimised structures in various different protonation states in order to complete our table of energies above.

So, first of all we need topology and coordinate files for our two protein structures in the de-protonated state. The FBP pdb files above have all the glutamic acid and aspartic acid residues defined as being in their de-protonated states (GLU and ASP) and so we can use these directly.

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
FBP1 = loadpdb FBP1.pdb
FBP2 = loadpdb FBP2.pdb

xleap should report that it added 288 hydrogens in each case. This is the number we are expecting.

All should be well apart from some close contact warnings and the fact that we have an unperturbed charge of -1.0. This will not matter since we will use a generalised born solvation model and simulate a weak salt solution of 0.2 Mol.

saveamberparm FBP1 FBP1_noH.prmtop FBP1_noH.inpcrd
saveamberparm FBP2 FBP2_noH.prmtop FBP2_noH.inpcrd

Note: since our two structures have the same topology and parameters the two prmtop files will be identical. Only the inpcrd coordinate files will differ.

Now we can go ahead and minimise these initial structures. Here is our input file for sander. This is very similar to tutorial two except that we will be simulating a salt concentration of 0.2 M since our system is not neutral and we will be using a large cut off of 20 angstroms.

Initial minimisation of our structures
&cntrl
imin=1, maxcyc=500, ncyc=200,
cut=20, ntb=0, igb=1, saltcon=0.2,
/

min.in

$AMBERHOME/exe/sander -O -i min.in -o FBP1_noH_min.out -p FBP1_noH.prmtop -c FBP1_noH.inpcrd -r FBP1_noH_min.crd &

$AMBERHOME/exe/sander -O -i min.in -o FBP2_noH_min.out -p FBP2_noH.prmtop -c FBP2_noH.inpcrd -r FBP2_noH_min.crd &

We can now extract the final energies from the minimisation and so fill in boxes A and B of our table.

                    FINAL RESULTS

   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    500      -1.5295E+03     3.9300E-01     3.7163E+00     NH2       371

 BOND    =       22.3884  ANGLE   =       61.8820  DIHED      =      300.1603
 VDWAALS =     -253.3185  EEL     =    -2555.4972  EGB        =     -947.8091
 1-4 VDW =      118.2634  1-4 EEL =     1724.4687  RESTRAINT  =        0.0000

                    FINAL RESULTS

   NSTEP       ENERGY          RMS            GMAX         NAME    NUMBER
    500      -1.5164E+03     4.6132E-01     4.0226E+00     HB3        66

 BOND    =       22.2754  ANGLE   =       60.6333  DIHED      =      305.9123
 VDWAALS =     -252.0156  EEL     =    -2696.2978  EGB        =     -810.6845
 1-4 VDW =      118.7859  1-4 EEL =     1735.0402  RESTRAINT  =        0.0000

Structure 1	PROTEIN NO H (A) -1529.5 KCal/mol	PROTEIN GLU 7 H (C)	PROTEIN GLU 10 H (E)	PROTEIN ASP 15 H (G)
Structure 2	PROTEIN NO H (B) -1516.4 KCal/mol	PROTEIN GLU 7 H (D)	PROTEIN GLU 10 H (F)	PROTEIN ASP 15 H (H)
		SOLUTION GLU NO H (I)	SOLUTION GLU H (K)
		SOLUTION ASP NO H (J)	SOLUTION ASP H (L)

Now we need to extract the final minimised structures from our two ensemble structures and then we can change the protonation states and calculate single point energies. First off we shall create pdb's of our minimised structures: