This is a brief introduction of how to use the PACE force field.
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Installation
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The package contains the following directories:

CGW/  
the topology file of CG water and a coordinate file of 216 pre-equilibrated CG water.

forcefiled/
all the parameters of the PACE force field. The organization of the parameter files are currently for GROMACS 3.x. However, the run file (.tpr) generated by GROMACS 3.x can be used with GROMACS 4.x, therefore entitling us the benefit of parallel improvement of GROMACS 4.x.

genpair/
a C code that is used to modify the topology file in order to use our PACE force field with GROMACS.

mdp/
the mdp files that describe simulation types and conditions; both the mdp files for normal MD and REMD are included.

example/
the coorinate files  (including water) for Gb1m2 and Trpcage peptides that studied in our paper.

First, please copy all the files in CGW/ and forcefield/ into the topology directories of your GROMACS software. Normally, it should be at gromacs/share/gromacs/top/. Then, please compile the C code at genpair/, by just typing "make". You should then have a program named as genPairPACE. Copy this program to your working directories.
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How to use the forcefield
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To build up a .tpr file that is needed by GROMACS, we first follow the standard procedure of GROMCAS:

first, assuming you have a protein coordinate in protein.PDB, you can generate .gro and .top files as follows:

pdb2gmx -f protein.PDB -o protein.gro -p protein.top -ter -ignh -vsite hydrogens 
 
When the program asks you to choose terminal groups, just select "none". The current model only handles blocked peptides at their terminus. In the .top file, the line "#include"spc.itp"" should be changed into "#include"cgWater.itp"" as we are not going to use all-atom water models. In addition, remember triple the mass of atoms in [ atoms ] section as described in the paper, in case you want to perform REMD simulations.

After that, you need to set the box of system

editconf -f protein.gro -o protein.gro -c -bt cubic -d 1.3 <= the smallest distance between box edges and protein, other values may be used, depending on your system.

Then fill the box with CG water:

genbox -cp protein.gro -cs cg216water -p protein.top -vdwd 0.235 -o proteinW.gro 

Then we need to generate a PDB file of protein that have the same order of atom indexes as the .top file, which will be used to modify the .top file for PACE. This can be done as follows:

pdb2gmx -f protein.PDB -o proteinPACE.PDB -ter -ignh -vsite hydrogens

Please check the numbers of residues [nr] and the number of atoms [na] in proteinPACE.PDB, and use genPACEPair we have compiled to generate an intermediate file that will be needed later:


./genPairPACE nr na proteinPACE.pdb > out.txt

Here out.txt is the file we want. It should have contents like:

---------------------------------------------
residuename CA:index/-1 CB: ......
...
residuename ....

[ exclusions ]
x1 y1
x2 y2
...
xn yn
[ pairs ]
x1 y1  1  C6_1 C12_1
...
xn yn  1  C6_n C12_n
[ impropers ]
...
--------------------------------------------------
You are almost there. Now you need to put the contents in the .top file. Specifically, you need to insert [ exclusions ] section into the protein.top, add [ pairs ] and [ impropers ]
sections into [ pairs ] and [ dihedrals ] sections of protein.top, respectively. Note that when you add [ pairs ] and [ impropers ], do NOT include "[ pairs ]" or "[ impropers ]". We also provide you an easier way of doing this. In genpair/, you can use a python script, insert_param.py, to finish the task. Given you have Python installed, you can generate the modified top as follows:

python insert_param.py out.txt protein.top > proteinPACE.top 

With the modified .top file, you can perform whatever simulations you want (with those .mdp files). 
 


  
