amber_tutorials/IntroductionMD/analysis_cpptraj.sh at main · freeenergylab/amber_tutorials · GitHub

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#!/usr/bin/env bash

module load amber/amber22_ambertools23

echo INFO: WORKDIR $PWD
echo INFO: HOSTNAME `hostname`
echo INFO: AMBERHOME $AMBERHOME

$AMBERHOME/bin/cpptraj -p complex.parm7 << EOF
trajin min2.rst7
autoimage
trajout min2_ascii.rst7
EOF

$AMBERHOME/bin/cpptraj -p complex.parm7 << EOF
trajin heat-3.rst7
autoimage
trajout heat-3_ascii.rst7
EOF

$AMBERHOME/bin/cpptraj -p complex.parm7 << EOF
trajin press-3.rst7
autoimage
trajout press-3_ascii.rst7
EOF

$AMBERHOME/bin/cpptraj -p complex.parm7 << EOF
trajin prod.rst7
autoimage
trajout prod_ascii.rst7
EOF

$AMBERHOME/bin/cpptraj -p complex.parm7 << EOF
trajin complex.rst7
trajin prod.nc 1 last 1
autoimage
trajout prod_autoimage_first_last.pdb pdb onlyframes 1,201
EOF

$AMBERHOME/bin/cpptraj -p complex.parm7 << EOF
trajin complex.rst7
trajin prod.nc 1 last 1
reference complex.rst7 [initial]
autoimage
rms ToInitial :1-14@CA ref [initial] out singleparticle_CA_rmsd.dat mass
rms ToInitialL :1-6@CA ref [initial] out single_CA_rmsd.dat mass nofit
rms ToInitialR :7-14@CA ref [initial] out particle_CA_rmsd.dat mass nofit
distance EndToEnd out end-to-end_dist.dat :1@CA :14@CA
radgyr RoG :1-14&!(@H=) out radius-of-gyration.dat mass nomax
atomicfluct RMSF out rmsf_backbone.dat @C,CA,N byres
trajout prod_rms_first_last.pdb pdb onlyframes 1,201
EOF

$AMBERHOME/bin/cpptraj -p complex.parm7 << EOF
trajin complex.rst7
trajin prod.nc 1 last 1
reference complex.rst7 [initial]
rms ToInitial :1-14 ref [initial] mass
strip :Na+
strip :WAT
trajout prod_solute_rms.pdb pdb
EOF