12. tleap#

 1#!/bin/bash
 2# Prepare topology/coordinate files 
 3# For protein, nucleic acid, and metal ion containing systems
 4# To add 12-6-4 LJ parameters, run:
 5#   bash parmed.sh
 6
 7SYS=$1 # FILENAME.pdb
 8
 9module load ambertools23
10
11tleap -f -<<_EOF
12source leaprc.protein.ff14SB
13source leaprc.DNA.OL15
14source leaprc.RNA.OL3
15source leaprc.water.tip3p 
16loadamberparams frcmod.ions234lm_1264_tip3p 
17
18sys = loadpdb ${SYS}
19
20savepdb sys step3_pbcsetup.pdb
21charge sys
22setbox sys vdw 
23
24saveamberparm sys step3_pbcsetup.parm7 step3_pbcsetup.ncrst
25savepdb sys step3_pbcsetup_wat.pdb
26
27quit
28
29_EOF

  • 12-6 parameters

 1#!/bin/bash
 2# Prepare topology/coordinate files 
 3# For protein, nucleic acid, and metal ion containing systems
 4# To add 12-6-4 LJ parameters, run:
 5#   bash parmed.sh
 6
 7SYS=$1 # FILENAME.pdb
 8
 9module load ambertools23
10
11tleap -f -<<_EOF
12source leaprc.protein.ff14SB
13source leaprc.DNA.OL15
14source leaprc.RNA.OL3
15source leaprc.water.tip3p 
16# loadamberparams frcmod.ions234lm_1264_tip3p 
17
18sys = loadpdb ${SYS}
19
20savepdb sys step3_pbcsetup.pdb
21charge sys
22solvatebox sys TIP3PBOX 12.0 iso 0.8 
23addions sys Na+ 0
24addions sys Cl- 0
25
26saveamberparm sys step3_pbcsetup.parm7 step3_pbcsetup.rst7
27savepdb sys step3_pbcsetup_wat.pdb
28
29quit
30
31_EOF

  • 12-6-4 parameters

 1#!/bin/bash
 2# Prepare topology/coordinate files 
 3# For protein, nucleic acid, and metal ion containing systems
 4# To add 12-6-4 LJ parameters, run:
 5#   bash parmed.sh
 6
 7SYS=$1 # FILENAME.pdb
 8
 9module load ambertools23
10
11tleap -f -<<_EOF
12source leaprc.protein.ff14SB
13source leaprc.DNA.OL15
14source leaprc.RNA.OL3
15source leaprc.water.tip3p 
16loadamberparams frcmod.ions234lm_1264_tip3p 
17
18sys = loadpdb ${SYS}
19
20savepdb sys step3_pbcsetup.pdb
21charge sys
22solvatebox sys TIP3PBOX 12.0 iso 0.8 
23addions sys Na+ 0
24addions sys Cl- 0
25
26saveamberparm sys step3_pbcsetup.parm7 step3_pbcsetup.rst7
27savepdb sys step3_pbcsetup_wat.pdb
28
29quit
30
31_EOF

  • tleap with small-molecule

 1#!/bin/bash
 2
 3module load ambertools23
 4
 5fname=$1
 6
 7if [ -z "${fname}" ]; then
 8    echo "NOT FOUND: PDB file of ligand!!!"
 9    exit 1
10fi
11
12if grep -q ".mol2" ${fname}; then
13    filename=$(awk -F '.' '{print $1}')
14    fileformat=$(awk -F '.' '{print $2}')
15elif grep -q ".pdb" ${fname}; then
16    echo "Please run antechamber to generate a mol2 file !!!"
17    exit 1
18else
19    echo "Assuming PDB file format..."
20    filename=${fname}
21    fileformat="mol2"
22fi
23
24tleap -f -<<_EOF
25source leaprc.protein.ff14SB
26source leaprc.water.tip3p
27source leaprc.gaff2
28
29LIG = loadmol2 ${filename}.${fileformat}
30
31check LIG
32
33loadamberparams ${filename}.frcmod
34saveoff LIG ${NAME}.lib
35saveamberparm LIG ${NAME}.parm7 ${NAME}.rst7
36
37quit
38
39_EOF

  • if PDB has waterbox already then you can set the box size

 1#!/bin/bash
 2
 3PROTEIN="protein"
 4LIGAND="lig"
 5ION="ion"
 6WATER="water"
 7
 8shopt -s expand_aliases
 9source ~/.bash_aliases
10mfa ambertools
11
12tleap -f -<<_EOF
13source leaprc.protein.ff14SB
14source leaprc.water.tip3p
15source leaprc.gaff2
16
17loadamberparams ${LIGAND}.frcmod
18loadoff ${LIGAND}.lib
19
20PROTEIN = loadpdb ${PROTEIN}.pdb
21LIG = loadmol2 ${LIGAND}.mol2
22ION = loadpdb ${ION}.pdb
23WAT = loadpdb ${WATER}.pdb
24
25SYS = combine { PROTEIN LIG ION WAT }
26
27set SYS box { 82.0 82.0 82.0 }
28check SYS
29
30savepdb SYS step3_pbcsetup.pdb
31saveamberparm SYS step3_pbcsetup.parm7 step3_pbcsetup.rst7
32
33quit
34
35_EOF
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