Solvate.sh

Wrapper script for Amber's LEaP ('tleap') to solvate a system with specific number of water molecules. Also makes use of cpptraj for determining molecule info.

Usage

Solvate.sh <input_file>
Input File Options: (default)
    target <#>         ) Target # of waters to add.
    buffer <buf>       ) Initial buffer size (10.0).
    bufx   <buf>       ) Initial buffer X size (mode 2|3 only, 10.0).
    bufy   <buf>       ) Initial buffer Y size (mode 2|3 only, 10.0).
    pdb <file>         ) Solute PDB file name.
    top <name>         ) Output topology (solvated.parm7).
    crd <name>         ) Output coordinates (solvated.rst7).
    leapin <file>      ) Leap input script for loading parameters etc.
    ionsin <file>      ) Optional Leap input for loading ions etc (run after solvating).
    templeap <name>    ) Name of temporary leap input script (temp.leap.in).
    tol <#>            ) Number of waters > target allowed, will be removed (2).
    mode <#>           ) Solvate mode:
                         (0)- SolvateOct
                          1 - SolvateBox
                          2 - SolvateBoxXYZ (bufx and bufy are scaled)
                          3 - SolvateBoxZ (bufx and bufy are fixed)
    loadpdb {yes|no}   ) If (yes), use 'loadpdb PDB'; otherwise <leapin> should set up unit <molname>.
    loadcmd <cmd>      ) Command to load solute file; default 'loadpdb'.
    soluteres <#>      ) Number of solute residues. If blank try to guess from PDB.
    molname <name>     ) Solute molecule unit name ('m').
    solventunit <name> ) Solvent unit (TIP3PBOX).
      Recognized solvent units: TIP3PBOX SPCBOX OPCBOX TIP4PEWBOX

First the file specified by leapin is read by LEaP, then the system is solvated, then the file specified by 'ionsin' is read in order to add ions etc.

Example

Solvate an RNA tetranucleotide with 2500 TIP3P waters and 3 Na+ ions.

Input file: solvate.in

# Target number of waters
target 2500 
# Initial guess for buffer
buffer 10
# Input PDB name
pdb rGACC.pdb
# Output topology name
top rGACC.tip3p.parm7 
# Output coordinates name
crd rGACC.nomin.rst7
# Base leap input script
leapin leap.solvate.in
# Additional script for adding ions etc
ionsin leap.ions.in
# Tolerance (# of waters off from target allowed)
tol 3
# 0 - SolvateOct
mode 0

LEaP input: leap.solvate.in

source leaprc.RNA.OL3
set default pbradii mbondi2

LEaP Ions input: leap.ions.in

addions m Na+ 1
addions m Na+ 1
addions m Na+ 1