Ambertools installation

Download AMBERTOOLS using following commands :

wget http://ambermd.org/downloads/install_ambertools.sh
# Or: curl http://ambermd.org/downloads/install_ambertools.sh -O
bash install_ambertools.sh -v 3 --prefix $HOME --non-conda

Export AMBERHOME path to .bashrc :
export AMBERHOME=/PATH/TO/amber17 ## for zsh or bash;
export PATH="${PATH}:${AMBERHOME}/bin"

OR source the path of AMBERHOME to .bashrc :
source /PATH/TO/amber17/amber.sh

Examples
Commands that can be used:
am1bcc
am1bcc -i mol.ac -f ac -o mol.ac
antechamber
antechamber -i g98.out -fi gout -o sustiva_resp.prep -fo prepi -c resp
antechamber -i g98.out -fi gout -o sustiva_bcc.prep -fo prepi -c bcc
antechamber -i g98.out -fi gout -o sustiva_gas.prep -fo prepi -c gas
antechamber -i g98.out -fi gout -o sustiva_cm2.prep -fo prepi -c cm2
antechamber -i g98.out -fi gout -o sustiva.ac -fo ac
antechamber -i sustiva.ac -fi ac -o sustiva.mpdb -fo mpdb
antechamber -i sustiva.ac -fi ac -o sustiva.mol2 -fo mol2
antechamber -i sustiva.mol2 -fi mol2 -o sustiva.gzmat -fo gzmat
antechamber -i sustiva.ac -fi ac -o sustiva_gas.ac -fo ac -c gas
atomtype
atomtype -i sustiva_resp.ac -o sustiva_resp_amber.ac -p amber
bondtype
bondtype -i sustiva.ac -o sustiva_bondtype.ac -f ac -j full
bondtype -i sustiva.mol2 -o sustiva_bondtype.ac -f mol2 -j part
crdgrow
crdgrow -i ref.pdb -o new.pdb -p sustiva_int.prep
database
database -i nci.sd -d define.dat
delphigen
delphigen -i sustiva_resp_at.ac -r sustiva.radius -c sustiva.crg -m sustiva.mpdb
espgen
espgen -i sustiva_g98.out -o sustiva.esp
parmcal

Usage

Please select:
1. calculate the bond length parameter: A-B
2. calculate the bond angle parameter: A-B-C
3. exit

parmchk
parmchk -i sustiva.prep -f prepi -o frcmod
prepgen
prepgen -i sustiva_resp_at.ac -o sustiva_int.prep -f int -rn SUS -rf SUS.res
prepgen -i sustiva_resp_at.ac -o sustiva_car.prep -f car -rn SUS -rf SUS.res
prepgen -i sustiva_resp_at.ac -o sustiva_int_main.prep -f int -rn SUS -rf SUS.res -m mainchain_sus.dat
prepgen -i ala_cm2_at.ac -o ala_cm2_int_main.prep -f int -rn ALA -rf ala.res -m mainchain_ala.dat
respgen
respgen -i sustiva.ac -o sustiva.respin1 -f resp1
respgen -i sustiva.ac -o sustiva.respin2 -f resp2
resp -O -i sustiva.respin1 -o sustiva.respout1 -e sustiva.esp -t qout_stage1
resp -O -i sustiva.respin1 -o sustiva.respout1 -e sustiva.esp -q qout_stage1 -t qout_stage2
antechamber -i sustiva.ac -fi ac -o sustiva_resp.ac -fo ac -c rc -cf qout_stage2
translate
translate -i nad.mol2 -f mol2 -o nad_trans.mol2 -c center -a1 0
translate -i nad.mol2 -f mol2 -o nad_match.mol2 -c match -r nad_ref.mol2
translate -i nad.mol2 -f mol2 -o nad_rotate.mol2 -c rotate2 -x1 0.0 -y1 0.0 -z1 0.0 -x2 1.0 -y2 0.0 -z2 0.0 -d 90.0
top2mol2
top2mol2 -p dna.prmtop -c dna.prmcrd -o dna.mol2
top2mol2 -p dna.prmtop -c dna.prmcrd -o dna_wat.mol2 -wt 1

Comments

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