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martinate.sh
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#!/bin/bash
PROGRAM=martinate.sh
VERSION=0.99
VERSTAG=devel-180428-1200-TAW
AUTHORS="Tsjerk A. Wassenaar, PhD"
YEAR="2018"
AFFILIATION="
University of Groningen
Nijenborgh 7
9747AG Groningen
The Netherlands"
: << __NOTES_FOR_USE_AND_EDITING__
IF YOU CHANGE THE PARAMETERS AND/OR WORKFLOW, PLEASE RENAME THE PROGRAM AND
STATE THE NATURE AND PURPOSE OF THE CHANGES MADE.
This has grown to be a rather complicated bash script. It is intended to
work through the MD process as a person would, issuing shell commands and reading
and editing files. Bash feels more natural for this than a Python/C wrapper.
It is advised to (get to) know about bash loops and variable substitution, as
these are used plenty. In addition, since there are many occassions where files
need to be read and edited, there are a lot of calls to sed, with quite a
few less ordinary commands.
To keep the code manageable, it is structured in sections and every section is
ordered, preferrably by numbered chunks. In addition, there is extensive
documentation. Every statement should be clear, either by itself or by a
preceding explanation. In case advanced bash/sed/... features are used, they
ought to be explained. That will keep the program manageable and make it a nice
place for learning tricks :)
Oh, and please note that usual copyright laws apply...
TAW - 20120718
(copied from gromit.sh)
__NOTES_FOR_USE_AND_EDITING__
DESCRIPTION=$(cat << __DESCRIPTION__
$PROGRAM $VERSION is a versatile wrapper built around
GROMACS, insane, and martinize, for setting up and running
MARTINI COARSE GRAIN molecular dynamics simulations of solvents,
membranes, proteins and/or nucleic acids in any combination.
It is built to allow automated processing of membrane proteins,
with full control of membrane composition. If no input file is provided,
only a membrane and/or solvent is built.
Options given that do not match an option in this script are passed to
martinize.py.
The script contains a complete and flexible workflow, consisting of the
following steps:
1. Generate topology from input structure
A. Generate atomistic topology (AA)
B. Generate MARTINI CG/multiscale topology (CG)
2. Solvation and adding ions (SOLVENT)
5. Energy minimization (EM)
6. Position restrained NVT equilibration (NVT-PR)
7. Unrestrained NpT equilibration (NPT)
8. Equilibration under run conditions (PREPRODUCTION)
9. Production simulation
A. Run input file (TPR)
B. Simulation (possibly in parts) (PRODUCTION)
The program allows running only part of the workflow by specifying the
start and end step (-step/-stop), using an argument uniquely matching
one of the tags given between parentheses.
This program requires a working installation of Gromacs. To link
the program to the correct version of Gromacs, it should be placed in the
Gromacs binaries directory or the Gromacs GMXRC file should be passed as
argument to the option -gmxrc
The workflow contained within this program corresponds to a standard protocol
that should suffice for routine CG molecular dynamics simulations of proteins
and/or nucleic acids in aqueous solution with or without a membrane.
It follows the steps that are commonly taken in MD tutorials
(e.g. those at http://cgmartini.nl).
This program is designed to enable high-throughput processing of CG molecular
dynamics simulations in which specific settings are varied systematically. These
settings include protein/nucleic acid, ligand, temperature, and pressure, as well
as many others.
## -- IMPORTANT -- ##
Molecular dynamics simulations are complex, with many contributing factors.
The workflow in this program has been tested extensively and used many times.
Nonetheless, it should not be considered failsafe. No MD protocol ever is.
Despite careful set up, simulations may crash, and the possibility that a crash
is encountered is larger when many simulations are run. If the run crashes,
the intermediate results will be kept and can be investigated to identify the
source of the problem.
If the run finishes to completion, this does not automatically imply that the
results are good. The results from the simulations should always be subjected
to integrity and quality assurance checks to assert that they are correct within
the objectives of the study.
__DESCRIPTION__
)
#--------------------------------------------------------------------
#---Parsing COMMAND LINE ARGUMENTS AND DEPENDENCIES--
#--------------------------------------------------------------------
CMD="$0 $@"
echo "$CMD" | tee CMD
# Directory where this script is
SDIR=$( [[ $0 != ${0%/*} ]] && cd ${0%/*}; pwd )
SRCDIR="$SDIR/source"
FFDIR="$SDIR/forcefield"
# Sourcing modules
source "$SRCDIR"/_logging.sh
source "${SRCDIR}"/_optionhandling.sh
source "${SRCDIR}"/_functions.sh
source "${SRCDIR}"/_mdp_martinate.sh
source "${SRCDIR}"/_mdp.sh
source "${SRCDIR}"/_mdrunner.sh
source "${SRCDIR}"/_pdb.sh
source "${SRCDIR}"/_martinate_index.sh
source "${SRCDIR}"/_martinate_multiscale.sh
source "${SRCDIR}"/_martinate_daft.sh
source "${SRCDIR}"/_gmx.sh
trap "archive" 2 9 15 # function archive in _functions.sh
# These will be looked for before running, and can be set from the cmdline, e.g.:
# -gmxrc /usr/local/gromacs-5.1/bin/GMXRC
# If not set, the default name will be searched for in
# 1. the environment (if PROGEVAR is given)
# 2. the directory where this calling script (martinate) is located
# 3. the PATH
DEPENDENCIES=( dssp gmxrc martinize insane liptop squeeze)
PROGEXEC=( dssp GMXRC martinize.py insane $FFDIR/liptop.py squeeze)
PROGEVAR=( DSSP GMXRC)
# Run control
MONALL= # Monitor all steps
CONTROL=
CHECKTIME=300 # Run control every five minutes
# Stepping stuff
STEPS=(AA CG SOLVENT EM NVT-PR NPT PREPRODUCTION TPR PRODUCTION ANALYSIS END)
get_step_fun() { for ((i=0; i<${#STEPS[@]}; i++)) do [[ ${STEPS[$i]} =~ ^$1 ]] && echo $i; done; }
STEP=AA
STOP=PRODUCTION
# MARTINI Force field parameters
MARTINI=martini22
DRY=
FFITP=
FFTAG=v2.0
USRITP=() # Additional topologies to include
# Solvents
# NOTE: with standard Martini water, exclude AA/CG interactions
SOLVENTS=( dry polarizable PW pw bmw W simple standard martini )
SOLNAMES=( NO PW PW PW BMW W W W W )
SOLTYPE=( NO polarizable polarizable polarizable polarizable plain plain plain plain )
EPSR_CG=( 15 2.50 2.50 2.50 1.30 15 15 15 15 ) # CG-CG dielectric constant
EPSR_AA=( 0 1.45 1.45 1.45 1.00 0 0 0 0 ) # CG-AA dielectric constant
SOLVFF=( dry p p p bmw ) # MARTINI subversion and solvent tag
# Options:
# Downstream programs:
# - membrane and periodic boundary conditions (insane options):
INSANE=()
# - martinizing
MARTINIZE=()
# This program:
# - protein:
PDB=
TOP=
NDX=
NOHETATM=true
VirtualSites=false
# - multiscaling
ForceField=gromos45a3
MULTI=()
ALL=false
M=false
NCH=0
SOL=
HybridIons=false
# - nonbonded interactions
EPSR=
EPSRF=78
LJDP=6
LJRP=12
LJSW=-1
RC=1.4
# - run control and files
DIR="." # Directory to run and write
TPR= # Run input file... skip to production or to STEP
NAME= # Run name
FETCH= # Try to fetch PDB file from web
MSGFILE=/dev/stdout # Master log file (stdout)
ERRFILE=/dev/stderr # Error log file (stderr)
EXEC= # Execute run
NP=1 # Number of processors
MDP= # User-provided MDP file
MDARGS= # User-provided arguments to mdrun
MAXH=-1 # Maximum duration of run
JUNK=() # Garbage collection
SCRATCH= # Scratch directory
ARCHIVE= # Archive file name
FORCE=false # Overwrite existing run data
KEEP=false # Keep intermediate rubbish (except junk)
DAFT=
# - system setup
Salinity=0.1536 # Salt concentration of solvent
# - group definitions
NATOMS=0 # Total number of atoms
Biomol=() # Biomolecules (protein, nucleic acid, lipid)
Solute=() # Solute molecule (protein or so)
Membrane=() # Lipids, excluding protein
Solvent=() # Solvent, including ions
Ligand=() # Ligands
Ligenv=() # Ligand environment to consider for LIE contributions
CoupleGroups=() # Groups for temperature coupling
EnergyGroups=() # Groups for energy calculations
LIE=false # LIE run
# - simulation parameters
TIME=0 # Production run time (ns)
AT=0.5 # Output frequency for positions, energy and log (ns)
DELT=0.020 # Time step in picoseconds
EMSTEPS=500 # Number of steps for EM
Temperature=310 # Degree Kelvin
Tau_T=0.1 # ps
Pressure=1 # Bar
Tau_P=1.0 # ps
SEED=$$ # Random seed for velocity generation
RotationalConstraints= # Use rotational constraints, which is mandatory with NDLP
# User defined gromacs program options and simulation parameters (way flexible!)
PROGOPTS=() # User-defined program options (--program-option=value)
MDPOPTS=() # User-defined mdp parametesrs (--mdp-option=value)
hlevel=0
olevel=0
# Collect errors, warnings and notes to (re)present to user at the end
# Spaces are replaced by the unlikely combination QQQ to keep the
# messages together.
errors_array=()
store_error_fun() { a="$@"; errors_array+=(${x// /QQQ}); FATAL "$@"; }
warnings_array=()
store_warning_fun() { a=$@; warnings_array+=(${x// /QQQ}); WARN "$@"; }
notes_array=()
store_note_fun() { a=$@; notes_array+=(${x// /QQQ}); NOTE "$@"; }
##>> OPTIONS
if [[ -z "$1" ]]; then
echo "No command line arguments give. Please read the program usage:"
USAGE 1
exit
fi
while [ -n "$1" ]; do
# Check for program option
depset=false
NDEP=${#DEPENDENCIES[@]}
for ((i=0; i<$NDEP; i++))
do
if [[ $1 == "-${DEPENDENCIES[$i]}" ]]
then
PROGEXEC[$i]=$2
shift 2
depset=true
fi
done
# If we set a dependency, skip to the next cycle
$depset && continue
# Check for other options
case $1 in
#=0
#=0 OPTIONS
#=0 =======
#=0
-h ) USAGE 0 ; exit 0 ;; #==0 Display help
--help ) USAGE 0 ; exit 0 ;; #==1 Display help
-hlevel ) hlevel=$2 ; shift 2; continue ;; #==1 Set level of help (use before -h/--help)
-olevel ) olevel=$2 ; shift 2; continue ;; #==1 Set level of options to display
#=1
#=1 File options
#=1 ------------
#=1
-f ) PDB=$2 ; shift 2; continue ;; #==0 Input PDB file
-g ) MSGFILE=$2 ; shift 2; continue ;; #==9 Standard output log file (default: /dev/stdout)
-e ) ERRFILE=$2 ; shift 2; continue ;; #==9 Standard error log file (default: /dev/stderr)
-name ) NAME=$2 ; shift 2; continue ;; #==9 Name of project
-top ) TOP=$2 ; shift 2; continue ;; #==1 Input topology file
-ndx ) NDX=$2 ; shift 2; continue ;; #==1 Input index file
-mdp ) MDP=$2 ; shift 2; continue ;; #==9 MDP (simulation parameter) file
-scratch ) SCRATCH=$2 ; shift 2; continue ;; #==9 Scratch directory to perform simulation
-fetch ) FETCH=$2 ; shift 2; continue ;; #==9 Database to fetch input structure from
-hetatm ) NOHETATM=false ; shift 1; continue ;; #==1 Keep HETATM records
#=1
#=1 Overall control options
#=1 -----------------------
#=1
-step ) STEP=$2 ; shift 2; continue ;; #==1 Step to start protocol
-stop ) STOP=$2 ; shift 2; continue ;; #==1 Step to stop protocol
-keep ) KEEP=true ; shift 1; continue ;; #==2 Whether or not to keep intermediate data
-dir ) DIR=$2 ; shift 2; continue ;; #==2 Directory for running simulation
-np ) NP=$2 ; shift 2; continue ;; #==1 Number of cores (processes) to use
-maxh ) MAXH=$2 ; shift 2; continue ;; #==2 Maximum run time
-force ) FORCE=true ; shift 1; continue ;; #==2 Whether or not to force redoing parts already run
-noexec ) EXEC=echo ; shift 1; continue ;; #==2 Whether or not to actually execute the commands
#=1
#=1 Forcefield control options
#=1 --------------------------
#=1
-cg ) MARTINI=$2 ; shift 2; continue ;; #==1 Coarse grain force field
-sol ) SOL=$2 ; shift 2; continue ;; #==1 Solvent type to use
-ffitp ) FFITP=$2 ; shift 2; continue ;; #==2 Coarse-grain force field definition
-ffdir ) FFDIR=$2 ; shift 2; continue ;; #==2 Directory for force field files
-fftag ) FFTAG=$2 ; shift 2; continue ;; #==2 Tag for force field files (v3.0 -> martini_v3.0_lipids.itp)
-itp ) USRITP+=($2) ; shift 2; continue ;; #==2 User-provided ITP file
-dry ) DRY=$2 ; shift 2; continue ;; #==2 Use dry martini from file definition
#=1
#=1 Simulation control options
#=1 --------------------------
#=1
-T ) Temperature=$2 ; shift 2; continue ;; #==1 Temperature
-P ) Pressure=$2 ; shift 2; continue ;; #==1 Pressure
-salt ) Salinity=$2 ; shift 2; continue ;; #==1 Salt concentration
-dt ) DELT=$2 ; shift 2; continue ;; #==2 Integration time step
-time ) TIME=$2 ; shift 2; continue ;; #==1 Production simulation time
-at ) AT=$2 ; shift 2; continue ;; #==1 Output sampling frequency
-em ) EMSTEPS=$2 ; shift 2; continue ;; #==2 Number of steps for EM
# -gmxrc ) GMXRC=$2 ; shift 2; continue ;;
# -dssp ) DSSP=$2 ; shift 2; continue ;;
-rtc ) RotationalConstraints=rtc ; shift ; continue ;; #==2 Whether or not to use rotational constraints
#=2
#=2 Multiscale options
#=2 ------------------
#=2
-m ) MULTI[$((NCH++))]=$2; M=true ; shift 2; continue ;; #==2 Chains for multiscaling
-M ) ALL=true; M=true ; shift 1; continue ;; #==2 Multiscale all chains
-ff ) ForceField=$2 ; shift 2; continue ;; #==2 Atomistic force field for multiscaling
-vsite ) VirtualSites=true ; shift 1; continue ;; #==2 Use virtual sites in multiscaling
-epsr ) EPSR=$2 ; shift 2; continue ;; #==2 Dielectric constant of vacuum
-epsrf ) EPSRF=$2 ; shift 2; continue ;; #==2 Dielectric constant of Reaction-Field
-ljdp ) LJDP=$2 ; shift 2; continue ;; #==2 Lennard-Jones dispersion
-ljrp ) LJRP=$2 ; shift 2; continue ;; #==2 Lennard-Jones repulsion
-ljsw ) LJSW=$2 ; shift 2; continue ;; #==2 Lennard-Jones switch radius
-rc ) RC=$2 ; shift 2; continue ;; #==2 Cut-off for non-bonded terms
#=1
#=1 Monitor options
#=1 ---------------
#=1
-monall ) MONALL=-monitor ; shift 1; continue ;; #==2 Monitor all steps using control script
-control ) #==2 Simulation monitor script
while [[ -n $2 && $2 != ';' ]]
do
CONTROL="$CONTROL $2"
shift
done
shift 2
echo MONITOR COMMAND: $CONTROL
continue;;
-ctime ) CHECKTIME=$2 ; shift 2; continue ;; #==2 Time for running monitor
#=2
#=2 A control process is either a program, script or command
#=2 that monitors the production run and terminates it
#=2 upon a certain condition, indicated by its exit code.
#=2
#=2 Protocol options
#=2 ----------------
#=2
-daft ) DAFT=$2; NDX=$2 ; shift 2; continue ;; #==2 Run martinate in DAFT pipeline
#=1
#=1 Advanced control options
#=1 ------------------------
#=1
#=2 This program allows specifying options for advanced control of
#=2 program invocation and simulation parameters. These options are
#=2 described below.
#=2
# The first one is the template/dummy for the help system
--mdp-option=value) olevel=2; hlevel=2; USAGE 1; continue;; #==2 Command-line specified simulation parameters
--mdp-* ) MDPOPTS+=(${1#--mdp-}) ; shift ; continue ;;
#=2
#=2 This will add 'option = value' to the MDP file for all simulations
#=2 following energy minimization. MDP options specified on the command line
#=2 take precedence over those specified in an input file (-mdp), which take
#=2 precedence over parameters defined in this script.
#=2 If the option takes multiple arguments, then 'value' should be a
#=2 comma separated list.
#=2 The STEP/STOP controls can be used to set parameters for (pre)production
#=2 simulations selectively.
#=2
# Options for downstream programs
# If the options are given on the command line, they are expanded and each
# option will be formatted as --program-opt=val
--martinize-option=value) olevel=2; hlevel=2; USAGE 1; continue;; #==2 Parameters for martinize
--martinize-*) MARTINIZE+=(${1#--martinize}) ; shift ; continue;;
--insane-option=value) olevel=2; hlevel=2; USAGE 1; continue;; #==2 Parameters for insane
--insane-*) INSANE+=(${1#--insane}) ; shift ; continue;;
# If the options are passed by another program, they will be formatted like
# --program{-opt1=val1,-opt2=val2\,val3}
# In this case the option needs to be parsed explicitly:
--martinize*) MARTINIZE+=($(readOptList $1)) ; shift ; continue;;
--insane*) INSANE+=($(readOptList $1)) ; shift ; continue;;
# Other program-specific options
--*) PROGOPTS[${#PROGOPTS[@]}]=$1 ; shift 1; continue ;;
#=0
#=0
# All options should be covered above. Anything else raises an error here.
*) BAD_OPTION "$1";;
esac
done
##<< OPTIONS
#--------------------------------------------------------------------
#---GLOBAL PARAMETERS AND STUFF--
#--------------------------------------------------------------------
exec 3>&1 4>&2
[[ -n $MSGFILE ]] && exec 1>$MSGFILE
[[ -n $ERRFILE ]] && exec 2>$ERRFILE
cat << __RUNINFO__
$PROGRAM version $VERSION:
(c)$YEAR $AUTHOR
$AFFILIATION
Now executing...
$CMD
__RUNINFO__
echo $CMD > cmd.log
# Time. To keep track of the remaining run time
START=$(date +%s)
# START/STOP FLOW CONTROL
for ((i=0; i<${#STEPS[@]}; i++)); do [[ ${STEPS[$i]} == ${STEP}* ]] && STEP=$i && break; done
for ((i=0; i<${#STEPS[@]}; i++)); do [[ ${STEPS[$i]} == ${STOP}* ]] && STOP=$i && break; done
# Set the scratch directory, if any:
# scratch directory, user name, random number
if [[ -n $SCRATCH ]]
then
# The scratch directory can be specified as
# (escaped) variable, like \$TMPDIR. This
# variable will be expanded at runtime.
# That may be handy on clusters, where the
# $TMPDIR is set for every node.
if [[ ${SCRATCH:0:1} == '$' ]]
then
tmp=${SCRATCH:1}
SCRATCH=${!tmp}
fi
# To ensure that there is no further rubbish
# the scratch directory is extended with the
# username, the data and the process ID. There
# the run will be performed.
SCRATCH=$SCRATCH/$(date +%F).$USER.$$
if ! mkdir -p $SCRATCH
then
echo Scratch directory $SCRATCH is not available... exiting
exit
fi
echo $SCRATCH > SCRATCH
fi
#--------------------------------------------------------------------
#---Sed and awk
#--------------------------------------------------------------------
# Awk expression for extracting moleculetype
# - at the line matching 'moleculetype'
# read in the next line
# continue reading next lines until one is not beginning with ;
# print the first field
AWK_MOLTYPE='/moleculetype/{getline; while ($0 ~ /^ *;/) getline; print $1}'
#--------------------------------------------------------------------
#---GROMACS AND RELATED STUFF
#--------------------------------------------------------------------
## 0. Finding programs
dependency_not_found_error()
{
FATAL The required dependency $@ was not found.
}
NDEP=${#DEPENDENCIES[@]}
find_program_function()
{
for ((i=0; i<$NDEP; i++)); do
if [[ ${DEPENDENCIES[$i]} == "$1" ]]
then
progr=${PROGEXEC[$i]}
envvar=${PROGEVAR[$i]}
fi
done
# Check if the program is in the environment
[[ -n $envvar ]] && [[ -f ${!envvar} ]] && echo ${!envvar} && return 0
# Check if the program is in the directory of this script
[[ -f $SDIR/$progr ]] && echo $SDIR/$progr && return 0
# Check if the program is in the PATH
# Python scripts may be available as 'binaries' (martinize/insane)
which $progr 2>/dev/null && return 0
which ${progr%.py} 2>/dev/null && return 0 || return 1
}
## 1. GROMACS ##
load_gromacs
## 2. DSSP ##
# Search the DSSP binary, from environment, from path, or guess
# Only required if we have an input file
SOLSTEP=$(get_step_fun CG)
if [[ $STEP -le $SOLSTEP && $STOP -ge $SOLSTEP ]]
then
echo -n '# Checking DSSP binary (for martinizing proteins)... '
DSSP=$(find_program_function dssp)
if [[ $? == 1 ]]
then
warn="DSSP binary not found - Will martinize without secondary structure :S"
store_warning_fun "$warn"
else
echo "$DSSP"
MARTINIZE+=(-dssp=$DSSP)
fi
fi
## 4. Echo mdp/program options specified on the command line
MSG="Program options specified on command line:"
echo_additional_options ${PROGOPTS[@]}
MSG="MDP options specified on command line (note how flexible!):"
echo_additional_options ${MDPOPTS[@]}
## 5. Locate insane if STEP lies before SOLVENT and STOP lies after.
SOLSTEP=$(get_step_fun SOLVENT)
if [[ $STEP -le $SOLSTEP && $STOP -ge $SOLSTEP ]]
then
INSA=$(find_program_function insane)
if [[ $? != 0 ]]
then
STEP=$NOW
FATAL "Dependency (insane) required for building solvent/membrane, but not found."
fi
fi
#--------------------------------------------------------------------
#---TIMING
#--------------------------------------------------------------------
# Maximum time in seconds
if [[ $MAXH =~ ":" ]]
then
# Format HH:MM:SS
ifs=$IFS; IFS=":"; MAXS=($MAXH); IFS=$ifs
MAXS=$((3600*MAXS[0] + 60*MAXS[1] + MAXS[2]))
else
# Format x.y HH
MAXS=$(awk '{printf "%d\n", $1*3600}' <<< $MAXH )
fi
if (( MAXS > 0 ))
then
UNTIL=$(( $(date +%s) + MAXS ))
echo "# $PROGRAM will run until $(date --date=@$UNTIL), or until run has finished"
else
echo "# No maximum runtime set. Will run until finished or until crash."
fi
# This variable will be reset to the time needed for the last run run
# A following run will usually take longer.
LASTRUN=0
#--------------------------------------------------------------------
#---WARMING UP VARIABLE GYMNASTICS
#--------------------------------------------------------------------
## 2. WORKING DIRECTORY AND SOURCE DIRECTORY ##
# SRCDIR=$(pwd)
[[ ! -d $DIR ]] && mkdir -p $DIR; pushd $DIR >/dev/null
## 3. START/STOP FLOW CONTROL ##
NOW=$STEP
echo "# Will run from step ${STEPS[$STEP]} until ${STEPS[$STOP]}"
## 4. SET THE SOLVENT ##
# Select the solvent to use
# Default solvent is martini water
if [[ -z $SOL ]]
then
if [[ $MARTINI == *p ]]
then
SOL=polarizable
fi
fi
SID=; for ((i=0; i<${#SOLVENTS[@]}; i++)); do [[ ${SOLVENTS[$i]} == ${SOL}* ]] && SID=$i; done
# Override if option -dry is given... Serving Dry Martini
[[ -n $DRY ]] && SID=0
# Check whether we found a matching solvent model
[[ -z $SID ]] && echo Unknown solvent model \"$SOL\" specified. && exit
# Check whether the solvent type is polarizable
[[ ${SOLTYPE[$SID]} == polarizable ]] && POLARIZABLE=true || POLARIZABLE=false
## 5. FORCE FIELD ##
# a. ATOMISTIC
# Set pointers to ffnonbonded.itp and ffbonded.itp if we do multiscaling
$M && ffnb=$GMXLIB/$ForceField.ff/ffnonbonded.itp || ffnb=
$M && ffbn=$GMXLIB/$ForceField.ff/ffbonded.itp || ffbn=
# b. COARSE GRAINED (MULTISCALE) ITP
# i. If a forcefield ITP is given, use that
# ii. If a forcefield ITP generating script is available use that
# iii. If $FFDIR contains a suitable forcefield ITP use that (and warn)
# iv. Raise an error
FFMARTINIPY=
if [[ -n $FFITP ]]
then
# i.
cp $FFITP ./martini.itp
else
FFMARTINIPY=$FFDIR/${MARTINI}${SOLVFF[$SID]}.py
if [[ ! -f $FFMARTINIPY ]]
then
if [[ -f $FFDIR/${MARTINI}.py ]]
then
# If martini22p was specified in stead of martini22 with PW,
# then we end up here, setting the script to martini22p.py
FFMARTINIPY=$FFDIR/${MARTINI}.py
fi
fi
if [[ -f $FFMARTINIPY ]]
then
# ii.
if [[ -n $DRY ]]
then
$FFMARTINIPY "$DRY" > martini.itp
else
$FFMARTINIPY $ffnb $ffbn > martini.itp
# UPDATE martini.itp FOR DUMMIES
# Replace the #include statement for ff_dum.itp for atomistic force fields by the contents of it
$M && $SED -i -e "/#include \"ff_dum.itp\"/r$GMXLIB/$ForceField.ff/ff_dum.itp" -e "/#include \"ff_dum.itp\"/d" martini.itp
fi
else
# iii.
# Check if an FF include exists in $FFDIR
FFITP=$(
for itp in $FFDIR/*itp
do
tags=$(grep '\[' $itp)
[[ "$tags" =~ defaults && "$tags" =~ atomtypes && "$tags" =~ nonbond_params ]] && echo $itp
done
)
if [[ -n $FFITP ]]
then
NOTE Found force field include file $FFITP
cp $FFITP martini.itp
fi
fi
fi
if [[ ! -f martini.itp ]]
then
FATAL Could not find forcefield itp file or generating script.
fi
# TODO - get something smarter for the FFTAG
if [[ "$MARTINI" =~ "martini3" ]]
then
FFTAG=v3.0
fi
## 6. ELECTROSTATICS AND TABLES ##
EPSR_CG=${EPSR_CG[$SID]}
EPSR_AA=${EPSR:-${EPSR_AA[$SID]}}
$M && TABLES=-tables || TABLES=
#--------------------------------------------------------------------
#---SIMULATION PARAMETERS--
#--------------------------------------------------------------------
## OT N ## For every parameter not defined the default is used
## NOTE ## This is probably fine for equilibration, but check the defaults to be sure
## E OT ## The list as is was set up for gromacs 4.5 and 5.1
init_mdp_parameters
read_mdp_file
read_mdp_options
#--------------------------------------------------------------------
#--------------------------------------------------------------------
#---SUBROUTINES--
#--------------------------------------------------------------------
ERROR=0
# Always ECHO the first line
NOW=$STEP
#--------------------------------------------------------------------
SHOUT "---= THIS IS WHERE WE START =---"
#--------------------------------------------------------------------
#--------------------------------------------------------------------
#---INPUT CHECKING, SPLITTING, TRIMMING, GROOMING
#--------------------------------------------------------------------
if [[ -n $PDB ]]
then
# If the input file is not found, check whether it was given without extension.
# If that is not the case, then fetch the file from the PDB repository.
if [[ ! -f $PDB ]]
then
PDB=$PDB.pdb
if [[ ! -f $PDB ]]
then
# Try fetching it from the PDB
pdb=$(tr [A-Z] [a-z] <<< ${PDB%.pdb})
fetch_structure $pdb $FETCH
[[ -n $SCRATCH ]] && cp $pdb.pdb $DIR
fi
fi
# If the input file is missing now, raise an errorr
if [[ ! -f $PDB ]]
then
echo Input file $PDB not found and fetching from PDB server failed.
exit 1
fi
# Check whether the input file is here or in another directory.
# In the latter case, copy it here
[[ $PDB == ${PDB##*/} || $PDB == ./${PDB##*/} ]] || cp $PDB .
pdb=${PDB##*/} # Filename
base=${pdb%.*} # Basename
ext=${pdb##*.} # Extension
dirn=${PDB%$pdb} # Directory
[[ $dirn ]] || dirn="."
dirn=`cd $dirn && pwd` # Full path to input file directory
if [ $dirn != `pwd` ]
then
NOTE "The run is performed here (`pwd`), while the input file is elsewhere ($dirn)."
fi
if [[ -z $TOP && $ext == "pdb" ]]
then
if $NOHETATM -a $(grep -q HETATM $PDB)
then
NOTE Removing HETATM entries from PDB file $PDB
$SED -i'' -e "/^HETATM/d" "$PDB"
fi
# Extract a list of chains from PDB file
CHAINS=( $(grep '^\(ATOM\|HETATM\)' $PDB | cut -b 22 | uniq) )
# Unpack lists of chains to multiscale separated by commas
MULTI=( $(for i in ${MULTI[@]}; do echo ${i//,/ }; done) )
# Residues defined in martinize.py
AA=(ALA CYS ASP GLU PHE GLU HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR)
# Sed query for residues (separated by \|):
SED_AA=$($SED 's/ \+/\\\|/g' <<< ${AA[@]})
# ATOM selection (martinizable residues)
ATOM='/^\(ATOM \|HETATM\)/{/.\{17\} *'$SED_AA' */p;}'
# HETATM selection (non-martinizable residues)
HETATM='/^\(ATOM \|HETATM\)/{/.\{17\} *'$SED_AA' */!p;}'
# Split the pdb file in stuff that can be processed with pdb2gmx
# and stuff that cannot be processed with it
# Extract the names of building blocks defined in the rtp file
# of the force field used. These blocks are defined as '[ ALA ]',
# so we match a name in square brackets at the start of a line.
# The name is appended to the hold space.
RTPENTRIES='/^\[ *\(...\).*\].*/{s//\1/;H;}'
# At the end of the list, the building block names are reformatted
# to make a regular expression string matching each word. First,
# the hold space is swapped with the pattern space, the first bit is
# removed and then all embedded newlines are replaced by '\|'
FORMAT='${x;s/\n...\n//;s/\n/\\\|/g;p;}'
# Finally sed is called processing all rtp files of the force field
DEF=$($SED -n -e "$RTPENTRIES" -e "$FORMAT" $GMXLIB/$ForceField.ff/*.rtp)
# Now we can split the input PDB file into a processable and a non-processable part
echo "# Defined building blocks in $ForceField RTP files:"
echo "# $DEF"
#sed -e '/^\(TER\|MODEL\|ENDMDL\)/p' -e '/^\(ATOM \|HETATM\)/{/.\{17\} *\('$DEF'\) */p;}' $dirn/$base.pdb > $base-def.pdb
#sed -e '/^\(TER\|MODEL\|ENDMDL\)/p' -e '/^\(ATOM \|HETATM\)/{/.\{17\} *\('$DEF'\) */!p;}' $dirn/$base.pdb > $base-ndef.pdb
fi
else
base=
fi
if [[ $PBC == retain && -n $PDB ]]
then
PBC="-pbc keep"
else
PBC="-pbc $PBC"
fi
echo "# Done checking"
echo "# Done gymnastics"
NOW=0
if [[ -n $DAFT ]] && ($ALL || [[ -n $MULTI ]])
then
echo "Currently, DAFTly splitting molecules in energy groups and running multiscaled is not possible."
echo "Will run using default multiscale splitting."
# Simply setting DAFT to false should disable any attempt to do splitting
DAFT=
fi
# Set the basename to 'membrane' if no input structure is given
[[ -n $PDB ]] || base=membrane
#---------------------------------------------------------------------
SHOUT "---STEP 1A: GENERATE ATOMISTIC STRUCTURE AND TOPOLOGY"
#---------------------------------------------------------------------
# Skip the atomistic topology if we do not multiscale
if ! $M && [[ $STEP == $NOW ]]
then
echo "Skipping step... (not multiscaling)"
: $((STEP++))
fi
# Skip this step if we run DAFT
if [[ -n $DAFT ]] && [[ $STEP == $NOW ]]
then
echo DAFT run. Skipping step.
: $((STEP++))
fi
if [[ $STEP == $NOW ]]
then
# Output for this section:
OUT=$base-aa.pdb
TOP=$base-aa.top
LOG=01-TOPOLOGY-AA.log
OUTPUT=($OUT $TOP)
# Delete existing output if we force this step
$FORCE && rm ${OUTPUT[@]}
if $(all_exist ${OUTPUT[@]})
then
echo Found $TOP and $OUT. Skipping structure/topology building with pdb2gmx...
: $((STEP++))
fi
fi
MDPMS=
ForceFieldAA=
if [[ $STEP == $NOW ]]
then
# I. Set the mdp tag
MDPMS=ms
# II. Atomistic force field for multiscaling
# 1. List force fields available
AAFF=($(ls -d $GMXLIB/*.ff | $SED 's#.*/\(.*\)\.ff#\1#'))
# 2. Try complete matching
for i in ${AAFF[@]}; do [[ "$i" == "$ForceField" ]] && ForceFieldAA=$i; done
# 3. Try partial matching if no complete match was found
match=0
[[ -n $ForceFieldAA ]] || for i in ${AAFF[@]}; do [[ $i =~ $ForceField ]] && ForceFieldAA=$i && : $(( match++ )); done
if [[ $match -eq 0 && -z $ForceFieldAA ]]
then
echo No matching atomistic forcefield found for $ForceField... Bailing out.
exit 1
elif [[ $match -gt 1 ]]
then
echo Ambiguous selection for atomistic force field... Bailing out.
exit 1
fi
# III. Interaction tables
TABLE="${SRCDIR}"/_table.py
# epsilon_r epsilon_rf cutoff LJ_dispersion LJ_repulsion LJ_cutoff LJ_switch
$TABLE $EPSR_CG $EPSRF $RC $LJDP $LJRP 1.2 0.9 > table.xvg