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0 parents commit 0843036f335745921a77ae21be0f5dedb1a34d4e @MaksMshn MaksMshn committed Jan 12, 2016
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  1. +2 −0 .gitignore
  2. +194 −0 README.md
  3. +7 −0 methane.pdb
  4. +1,259 −0 rism3d_pc.py
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+PC+
+===
+
+Python script to simplify computation of 3D-RISM pressure corrected (PC+) hydration free energy.
+
+Authors
+-------
+Maksim Mišin <mishin1991@gmail.com>
+
+Usage examples
+--------------
+
+As an input script takes a pdb file with single solute. For example (methane.pdb):
+```text
+ATOM 1 C1 MOL 1 3.537 1.423 0.000 1.00 0.00
+ATOM 2 H1 MOL 1 4.089 2.224 0.496 1.00 0.00
+ATOM 3 H2 MOL 1 4.222 0.611 -0.254 1.00 0.00
+ATOM 4 H3 MOL 1 2.759 1.049 0.669 1.00 0.00
+ATOM 5 H4 MOL 1 3.077 1.810 -0.912 1.00 0.00
+TER
+END
+```
+
+1) 298.15 K methane hydration free energy calculation:
+
+```bash
+$ python rism3d_pc.py methane.pdb
+Starting SFE calculation for methane.pdb at T=298.15 K
+Running AM1-BCC calculation...
+Running 1D-RISM calculation...
+Running 3D-RISM calculation...
+Calculation has finished
+RISM exchem=8.57636028 kcal/mol
+PC+ dG*(hyd)=1.07928069898 kcal/mol
+Detailed output can be found in methane_298.15/methane.log
+```
+
+2) 350 K calculation with tip3p water
+
+```bash
+$ python rism3d_pc.py methane.pdb -t 350 --smodel TP3
+Starting SFE calculation for methane.pdb at T=350.0 K
+Running AM1-BCC calculation...
+Running 1D-RISM calculation...
+Running 3D-RISM calculation...
+Calculation has finished
+RISM exchem=9.01341914 kcal/mol
+PC+ dG*(hyd)=1.35551076507 kcal/mol
+Detailed output can be found in methane_350.0/methane.log
+```
+
+3) Using existing topology and susceptibility (xvv) files
+
+```bash
+$ python rism3d_pc.py methane.pdb -p methane.prmtop -x water_nacl.xvv
+Starting SFE calculation for methane.pdb at T=298.15 K
+Reading user provided prmtop file
+Using provided xvv file...
+Running 3D-RISM calculation...
+Calculation has finished
+RISM exchem=8.67168499 kcal/mol
+PC+ dG*(hyd)=1.1103088454 kcal/mol
+Detailed output can be found in methane_298.15/methane.log
+```
+
+Prerequisites
+-------------
+
+The script requires:
+
+* Python 2.7 or later: http://www.python.org/
+* AmberTools13 or later: http://ambermd.org/
+
+
+Get some help
+-------------
+
+ $ python rism3d_pc.py -h
+ usage: rism3d_pc.py [-h] [-p PRMTOP] [--scale_chg SCALE_CHG] [-c MOLCHARGE]
+ [--multiplicity MULTIPLICITY] [--minimize MINIMIZE]
+ [-x XVV] [--smodel SMODEL] [--rism1d RISM1D]
+ [--closure [CLOSURE [CLOSURE ...]]] [-t TEMPERATURE]
+ [--clean_up CLEAN_UP] [--dir_name DIR_NAME]
+ [--timeout TIMEOUT]
+ [--tolerance [TOLERANCE [TOLERANCE ...]]] [--write_g]
+ [--write_c] [--write_u] [--write_asymp] [--noasympcorr]
+ [--buffer BUFFER] [--solvbox SOLVBOX SOLVBOX SOLVBOX]
+ [--grdsp GRDSP GRDSP GRDSP] [--polar_decomp]
+ [--verbose3d VERBOSE3D] [--maxstep3d MAXSTEP3D]
+ molec.pdb
+
+ Run 3D-RISM single point calculation. This script is a wrapper around Amber
+ rism3d.snglpnt program, designed to simplify calculations. It also computes
+ pressure corrections to RISM solvation free energy.
+
+ optional arguments:
+ -h, --help show this help message and exit
+
+ Solute options:
+ Options related to a solute molecule. Calculation requires only pdb and
+ prmtop files. If prmtop file is not present, script will try to create
+ this file using antechamber and tleap. By default AM1-BCC charges and GAFF
+ will be used.
+
+ molec.pdb Input solute file. Must be in pdb format acceptable by
+ Antechamber. Must have a .pdb extension.
+ -p PRMTOP, --prmtop PRMTOP
+ Path to parameters and topology (prmtop) file of
+ solute.
+ --scale_chg SCALE_CHG
+ Scale all solute by this value prmtop file [1.0].
+ -c MOLCHARGE, --molcharge MOLCHARGE
+ Charge of the solute [0].
+ --multiplicity MULTIPLICITY
+ Multiplicity of the solute [1].
+ --minimize MINIMIZE Minimize solute before performing 3D-RISM calculation
+ using either gradient descent (min) or RISM
+ minimization using sander (rism, not recommended). If
+ no keywords are provided minimization is not
+ performed.
+
+ 1D-RISM options:
+ 3D-RISM calculation requires xvv file (site-site susceptibilities) to run.
+ If such file is not provided script can run a 1D-RISM to try to genrate
+ it, but will asume that the solvent is pure water. Some of the 1D-RISM
+ related options are in 3D-RISM group.
+
+ -x XVV, --xvv XVV Path to an existing xvv file. This will skip 1D-RISM
+ calculation and all related parameters will be
+ ignored. Solvent density as well as calculation
+ temeprature will be read from this file.
+ --smodel SMODEL Solvent model for 1D-RISM calculation available in
+ "$AMBERHOME/dat/rism1d/model/{smodel}.mdl" [SPC].
+ --rism1d RISM1D Type of 1D-RISM theory. Only DRISM has been
+ extensively tested [DRISM].
+
+ 3D-RISM options:
+ Options related to the main calculation.
+
+ --closure [CLOSURE [CLOSURE ...]]
+ Brdige closure for 3D-RISM and 1D-RISM calculation if
+ it is necessary. Either HNC, KH, PSEn (n in PSEn
+ should be an integer) or a list of them for sequential
+ convergence. For 1D-RISM calculation only last closure
+ will be used [PSE3].
+ -t TEMPERATURE, --temperature TEMPERATURE
+ Temperature in K at which calculation will be
+ preformed. If xvv file was provided, this option will
+ be used only for naming directory [298.15].
+ --clean_up CLEAN_UP How should auxiliary files be treated: 0 - delete
+ nothing; 1 - delete some [default]; 2 - delete all but
+ input, results, and log.
+ --dir_name DIR_NAME Custom name for produced calculation directory. The
+ default one is: {mol_name}_{temperature}.
+ --timeout TIMEOUT Minutes after which 3D-RISM calculation will be
+ killed. Use 0 for no timeout. [0]. Only works on Unix-
+ like system.
+ --tolerance [TOLERANCE [TOLERANCE ...]]
+ Maximum residual values for 3D-RISM solution
+ convergence. If many closures a list of closures can
+ be supplied [1E-5].
+ --write_g Write radial distribution functions produced in 3D-
+ RISM calculation.
+ --write_c Write direct correlation function produced in 3D-RISM
+ calculation.
+ --write_u Write solute solvent potential energy grid.
+ --write_asymp Write asymptotics of total and direct correlation
+ fuctions in real space.
+ --noasympcorr Thermodynamics of 3D-RISM is calculated without long-
+ range asymptotics.
+ --buffer BUFFER Minimum distance between the solute and the edge of
+ the solvent box in A for 3D-RISM calculation [25].
+ --solvbox SOLVBOX SOLVBOX SOLVBOX
+ Size of the x, y, and z dimensions of the box in
+ Angstroms. Specifying this parameter overrides buffer.
+ --grdsp GRDSP GRDSP GRDSP
+ Linear grid spacings for x, y and z dimensions. Should
+ be separated with spaces. Units: A [0.5 0.5 0.5].
+ --polar_decomp Decomposes solvation free energy into polar and non-
+ polar components.
+ --verbose3d VERBOSE3D
+ Verbosity of 3D-RISM calculation. 0 - print nothing; 1
+ - print iterations; 2 - print all [2].
+ --maxstep3d MAXSTEP3D
+ Maximum number of iterations in 3D-RISM calculation
+ [500].
+
+
+Notes
+-----
+The script has been tested only on Ubuntu, but it should work on most Linux distributions and on Mac OS X. To make it Windows-friendly one would probably need to change the names of executable programs and add them to the PATH.
+
+
+
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+ATOM 1 C1 MOL 1 3.537 1.423 0.000 1.00 0.00
+ATOM 2 H1 MOL 1 4.089 2.224 0.496 1.00 0.00
+ATOM 3 H2 MOL 1 4.222 0.611 -0.254 1.00 0.00
+ATOM 4 H3 MOL 1 2.759 1.049 0.669 1.00 0.00
+ATOM 5 H4 MOL 1 3.077 1.810 -0.912 1.00 0.00
+TER
+END
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