This program is used to setup a ProtoMS simulation. It was made with usability at highest priority. The only input that should be necessary is a couple of prepared PDB files containing the molecules one would like to simulate.
The program will create force field for small molecules, setup the protein and solvate the prepared system. At the moment it can setup the following types of simulations:
The program will create files and inputs based on experience that should work in most situations. However there might be situations where the created settings are not appropriate. One can then use individual tools to make a more custom setup, see this. One might also have to edit the files manually.
Syntax:
protoms.py [-s none|equilibration|sampling|dualtopology|singletopology|gcmc|jaws1|jaws2] [-f folder1 folder2] [-p protein.pdb] [-sc scoop.pdb] [-l lig1.pdb lig2.pdb ...] [-t template1 template2 ...] [-w water.pdb] [-c cmdfile] [-r nrepeats | prefix] [--outfolder folder] [--atomnames namefile] [--watmodel tip4p|tip3p] [--waterbox watbox] [--charge charge1 charge2] [--singlemap mapfile] [--center cent] [--innercut icut] [--outercut ocut] [--flexin sidechain|flexible|rigid] [--flexout sidechain|flexible|rigid] [--scooplimit N] [--capradius radius] [--lambdas nlambdas | lambda1 lambda2 ...] [--adams B1 B2 ...] [--jawsbias bias] [--gcmcwater wat.pdb | N] [--gcmcbox box.pdb | X Y Z A B C] [--nequil N] [--nprod N] [--dumpfreq N] [--absolute] [--dovacuum] [--testrun] [--cleanup]
optional, default = none
optional, no default
optional, no default
optional, no default
optional, no default
optional, no default
optional, no default
optional, default = run
optional, default = 1 nrepeat = repeats a created from 1 to nrepeat prefix = a single repeat is created, but prefix is appended to folders and files
optional, default = "" (empty string)
optional, no default if not given, takes the one in $PROTOMSHOME/data
optional, default = tip4p
optional, no default if not given, takes one in $PROTOMSHOME/data
optional, default = 0
optional, no default
optional, default = 0.0,0.0,0.0
optional, default = 16.9 A
optional, default = 20.0 A
optional, default = flexible sidechain = only the sidechains will be sampled in the simulation flexible = both sidechain and backbone will be sampled in the simulation rigid = no residues will be sampled
optional, default = sidechain sidechain = only the sidechains will be sampled in the simulation flexible = both sidechain and backbone will be sampled in the simulation rigid = no residues will be sampled
optional, default = 10
optional, default = 30
optional, default = 16
if a single value is given, this number of -values is created uniformly from 0 to 1
if a list of values are given, this is the
-values to use
optional, default = 0
optional, default = 0
optional, no default if an integer is given this corresponds to the number of water to add to the GCMC/JAWS-1 box
optional, no default if six numbers are given this corresponds to the origin (first three) and the length (last three) of the box
optional, default = 5E6
optional, default = 40E6
optional, default = 1E5
optional, default = off
optional, default = off
optional, default = off
optional, default = off
Examples:
protoms.py
protoms.py.py -s sampling -l lig1.pdb --dovacuum --testrun
protoms.py -s dualtopology -l lig1.pdb lig2.pdb -p protein.pdb
protoms.py -s dualtopology -l lig1.pdb --absolute
protoms.py -s gcmc -p protein.pdb --adams -4 -2 0 2 4 6
Notes:
The program will try to locate previously created files for the protein and ligand in the current working directory or any folder specified with the -f flag. For ligands the program will replace .pdb with the appropriate ending, such as .prepi for Amber prepi files and .tem for ProtoMS template files.
Starting with just the PDB-files of the ligand(s) and the protein, the program will create the following files in the same folder as those PDB-files
lig.prepi = the z-matrix and atom types of the ligand in Amber format
lig.frcmod = additional parameters not in GAFF
lig.zmat = the z-matrix of the ligand used to sample it in the MC simulation
lig.tem = the complete template (force field) file for the ligand in ProtoMS format
the filename is a combination of the residue name of all ligands
lig_box.pdb = the box of water solvating the ligand
protein_scoop.pdb = the truncated protein structure
if the scoop removes to few residues, this file be created instead
water.pdb = the cap of water solvating the protein system
In addition, for dual-topology simulations the following files are created: :
only created if the –absolute flag is set
In addition, for single-topology simulations the following files are created:
li1-li2_ele.tem = the ProtoMS template file for electrostatic single-topology perturbation
li1-li2_vdw.tem = the ProtoMS template file for van der Waals single-topology perturbation
li1-li2_comb.tem = the ProtoMS template file for combined/single-step single-topology perturbation
only named like this if the –singlemap argument is not set
In addition, for GCMC / JAWS-1 simulations the following files are created:
In addition, for JAWS-2 simulations the following files are created:
each of the water given with the --gcmc_water flag will be written to an individual file
jaws2_notN.pdb = the rest of the JAWS-2 water
water_clr.pdb = the cap of water solvating the protein system, cleared from the GCMC / JAWS-1 simulation box
It will create at most three ProtoMS command files, one for the protein simulation, one for the ligand simulation and one for the gas-phase simulation. These can be used to run ProtoMS, e.g.
$PROTOMS/protoms3 run_free.cmd
Prerequisites:
The program assumes that both the ligand and the protein is prepared before. This includes for instance protonation. At the moment only Amber naming convention is supported.
The progam requires AmberTools to make force field for small molecules.