(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 2008

Building your own Custom Residues (old version) - SECTION 4

Simulating a Solvated Protein that Contains Non-Standard Residues
(Simple Version)

By Ross Walker

Stage 4 - Creating the Prmtop and Inpcrd files

In order to introduce the new parameters we have two options. We can modify the main force field files or we can create an frcmod file with the changes specific to this project. The second option is a much better choice since modifying the main files could lead to clashes with other people who use the same installation. Creating a set of parameters is a bit of an art, since one is often faced with unknown parameters (such as force constants for copper to its ligands as in this example). The purpose of this tutorial is simply to cover the mechanics of running AMBER and so I provide you all of the parameters below. Note, these are for tutorial purposes only, I make no claims about the validity or appropriateness of these parameters. There are a number of articles in the literature about parameter estimation, and users are encouraged to consult them when faced with unusual chemical environments. A starting point is section 12.1 of the AMBER 8 manual entitled Parameter Development.

Here is the frcmod file I have created for plastocyanin:

#  modifications to force field for poplar plastocyanin  

MASS
CU 65.36

BOND 
NB-CU  70.000   2.05000 #kludge by JRS    
CU-S  70.000   2.10000 #kludge by JRS    
CU-SH  70.000   2.90000 #for pcy    
CT-SH 222.000   1.81000 #met(aa)   

ANGLE   
CU-NB-CV   50.000     126.700  #JRS estimate    
CU-NB-CR   50.000     126.700  #JRS estimate   
CU-NB-CP   50.000     126.700  #JRS estimate   
CU-NB-CC   50.000     126.700  #JRS estimate   
CU-SH-CT   50.000     120.000  #JRS estimate   
CU-S -CT   50.000     120.000  #JRS estimate    
CU-S -C2   50.000     120.000  #JRS estimate    
CU-S -C3   50.000     120.000  #JRS estimate    
NB-CU-NB   10.000     110.000  #dac estimate    
NB-CU-SH   10.000     110.000  #dac estimate    
NB-CU-S    10.000     110.000  #dac estimate   
SH-CU-S    10.000     110.000  #dac estimate  
CU-SH-CT   50.000     120.000  #JRS estimate 
CT-CT-SH   50.000     114.700    #met(aa)  
HC-CT-SH   35.000     109.500   
H1-CT-SH   35.000     109.500  
CT-SH-CT   62.000     98.900  #MET(OL)  

DIHE 
X -NB-CU-X    1       0.000 180.000       3.000    
X -CU-SH-X    1       0.000 180.000       3.000   
X -CU-S -X    1       0.000 180.000       3.000   
X -CT-SH-X    3       1.000   0.000       3.000   

NONBON 
CU    2.20      0.200   

Anything with a # in front of it is a comment. As you can see we specify the mass, missing bonds, angle and dihedrals as well as VDW parameters.

We can now load this file into xleap and it will add all of these parameters to the PARM99 force field we selected.

$AMBERHOME/exe/xleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99
> loadamberparams plc.frcmod
> loadoff 1PLC.lib

We should now be able to create our topology and coordinate files.

> saveamberparm 1PLC 1PLC.prmtop 1PLC.inpcrd

Here are the files: 1PLC.prmtop, 1PLC.inpcrd

If you wish to look at the starting structure in vmd we can use ambpdb to create a pdb file for us:

$AMBERHOME/exe/ambpdb -p 1PLC.prmtop < 1PLC.inpcrd > 1PLC.inpcrd.pdb

Here it is: 1PLC.inpcrd.pdb

We could now use these files to run plastocyanin simulations. You can try this yourself if you want. Just remember that this is in explicit solvent and a peridiodic box so you use periodic boundary conditions. You will also need to minimise the system initially to remove bad contacts. I would then heat it over 20ps from 0 to 300K with constant volume periodic boundaries before moving to a long equilibration at 300 K with constant pressure.

(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 2008