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

How to keep chain ID / IDs in GROMACS?

In GROMACS , while converting pdb file (monomer or multimer) into .gro file, it do not preserve the chain ID information. Due to the lack of chain ID information, pdb file retrieved from .gro file at any stage of the simulation has missing chain IDs and pdb file can not be visualized properly in PYMOL / RASMOL . There are two ways to convert .gro file into .pdb Lets say your protein name is xyz.pdb 1] gmx editconf -f xyz.gro -o xyz.pdb 2] gmx trjconv -f xyz.gro -o xyz.pdb -s xyz.tpr Only ' trjconv ' will retrieve the chain ID information for all the chains. and not ' editconf '. If you have monomer protein and wish to assign any chain ID then following command will be of your interest: gmx editconf -f xyz.gro -o xyz.pdb -label [ chain-ID ]

Python : Turtle tree

Turtle module can be used to draw some very nice patterns in Python. Following are some examples with code. ==================== import turtle import random t = turtle.Turtle( shape = "circle" ) t.lt( 90 ) lv = 14 l = 120 s = 30 t.color( 'indigo' ) t.width(lv) t.penup() t.bk(l) t.pendown() t.fd(l) def draw_tree ( l , level ): width = t.width() # save the current pen width t.width(width * 3.0 / 4.0 ) # narrow the pen width l = 3.0 / 4.0 * l #t.color(R,G,B) #provide the RGB numbers t.color(random.random(), random.random(), random.random()) t.lt(s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.rt( 2 * s) t.fd(l) if level < lv: draw_tree(l, level + 1 ) t.color(random.random(), random.random(), random.random()) t.bk(l) t.lt(s) t.width(width) # restore the previous pen width t.speed( "fastest" ) draw_tree(l, 5 ) turtle.done() ===========

GNUPLOT: How to draw trend line?

How to draw trend line in the GNUPLOT? If you like to plot graphs in gnuplot and dont know how to plot trendline then here you are. Follow the steps mentioned below... 1. You should have a files with X and Y values 2. Open GNUPLOT (Operating system dosen't change anything here. It works on all systems) 3. Type the command in the gnuplot terminal Lets say I have a file for eg. '1.txt' p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth acsplines title '1.txt' OR p '1.txt' u 1:2 w d title '', '1.txt' u 1:2 smooth bezier title '1.txt' It will plot as below...

How to use MODELLER to build DIMER homology model with ligand?

How to use MODELLER to build DIMER homology model with ligand? Procedure: Get Fasta sequence from UNIPROT database. Predict sequence alignment from HHPRED Prepare INPUT files for MODELLER model-dimer.py (Click to download) ############### from modeller import * from modeller.automodel import * #from modeller import soap_protein_od env = environ() env.io.hetatm = True a = automodel(env, alnfile='TvLDH-1bdm.ali', knowns='1bdm', sequence='TvLDH', assess_methods=(assess.DOPE, #soap_protein_od.Scorer(), assess.GA341)) a.md_level = refine.very_slow a.starting_model = 1 a.ending_model = 1 #Number of output models a.final_malign3d = True a.make() ################ TvLDH-1bdm.ali (Click to download) (Alignment taken from SALI LAB) >P1;1bdm structureX:1bdm.pdb: 0: A: 333: B:u

Plagarism Checker

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