[AMBER] Save RST from mdcrd containing velocities

From: Yuliana Bosken <ydavi002.ucr.edu>
Date: Sat, 13 Apr 2019 02:40:05 -0700

Hi,
I have a trajectory 20000 steps (2fs ts for a total of 20 ns) containing
velocities. I want to save for example every 1000th step as rst file so I
can restart separate MD runs from each. I tried ptraj input file which
seems to only allow to convert to dcd and pdb, but the pdb I generated
contains all frames and I need the 20 separate rst files:
Here are the options available and part of the script:
INPUTFILENAME=(
"md01.mdcrd"
)
OUTPUTFILENAME="frame.pdb"
OUTPUTFORMAT="pdb"
PRMTOPFILENAME="../02.add_water/water.prmtop"
# velocity
VELOCITY="1"
# nobox
NOBOX="0"
# ADVANCED=1 to turn on selection, =0 to turn off
ADVANCED="1"
START="1"
FINAL="50000000"
FREQ="1000"
# UNWRAP=1 to unwrap
UNWRAP="0"
RESIDUE="1-269"
CENTER="1-269"
# STRIPWATER=1 to strip water
STRIPWATER="0"
STRIPWATER_FLAG="WAT"
STRIPION1="0"
STRIPION1_FLAG="Cl-"
STRIPION2="0"
STRIPION2_FLAG="Na+"
.....
if [ $OUTPUTFORMAT = "dcd" ]; then
    format="charmm"
elif [ $OUTPUTFORMAT = "mdcrd" ]; then
    format="trajectory"
elif [ $OUTPUTFORMAT = "netcdf" ]; then
    format="netcdf"
elif [ $OUTPUTFORMAT = "pdb" ]; then
    format="pdb"
fi

if [ $format = "" ]; then
    echo "Format Not Supported"
else
    TRAJIN=""
    for ix in ${!INPUTFILENAME[*]}
    do
        TRAJIN="$TRAJIN
trajin ${INPUTFILENAME[$ix]} $argument"
    done
    echo "$TRAJIN
trajout $OUTPUTFILENAME $format $NOBOX $VELOCITY $argument3 $argument2" >
$tempfilename
    cpptraj $PRMTOPFILENAME $tempfilename
    rm $tempfilename
fi
Thank you in advance!
Yuliana

-- 
Yuliana Bosken
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Received on Sat Apr 13 2019 - 03:00:02 PDT
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