Amber参考

2017-09-01

准备protein和ligand

#####ligand

1	acpype -i x.mol2 -n 0 # -n: net charge

ligand

branch 1 for BCC
   antechamber -i raw.pdb|mol2 -fi pdb|mol2 -o lig.mol2 -fo mol2 -c resp|bcc
   parmchk2    -i lig.mol2 -f mol2 -o lig.frcmod
branch 2 for RESP
   antechamber -i lig.mol2 -fi mol2 -o lig.in -fo gzmat
   g092 lig.i
   antechamber -i lig.out  -fi gout -o lig.prep -fo prepi -c resp|bcc
branch 1 for Gromacs
   directly copy charge from prep into itp file
branch 2 for Amber (and then convert into Gromacs)
   parmchk2    -i lig.prep -f prepi -o lig.frcmod
   sleap #generate top and crd from mol2 and frcmod
   acpype -p x.parmtop -x x.inpcrd -d -n 1  # -n: net charge  # after tleap

protein (+ligand)

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hand-edit pdb file
pdb4amber -i old.pdb -o new.pdb -reduce -dry (remove water) (ambpdb)
reduce

tleap命令:
source leaprc.protein.ff14SB
source leaprc.DNA.OL15
source leaprc.RNA.OL3
source leaprc.lipid17
source leaprc.GLYCAM_06j
source leaprc.gaff2
source leaprc.water.tip3p   
list
check
copy
load/save+pdb/off/amberparams
lig = loadmol2 lig.mol2       # must with charge antechamber -i mol2 -o mol2 -c bcc
loadamberparams lig.frcmod    # 小分子立场参数缺失文件
saveoff lig lig.lib
saveamberparm lig lig.prmtop lig.inpcrd
loadoff lig.lib
loadamberparams lig.frcmod 
model= sequence {ACE ALA NME}
  # ALA, ARG, ASN, ASP, CYS|CYX, GLU, GLN, GLY, HID|HIE|HIP, ILE,
  # LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, N***, C***, 
  # DA, DT, DG, DC, RA, RU, RC, RG,
edit model
model=loadpdb x.pdb   #include ligand with the same name as lig.lib
check|edit|combine model
desc model
desc model.1
desc model.ALA
bond model.1.SG  model.6.SG 
charge model 
addions model Na+ 0  
solvatebox|solvateoct model TIP3PBOX 8.0 
model3=combine {model1 model2}
model4=copy model3
saveamberparm model x.top x.crd
savepdb model x.pdb
quit

1 2	# if convert top and crd into top and gro acpype -p x.parmtop -x x.inpcrd -d -n 1 # -n: net charge # after tleap

Nucleic acid

nab.exe:

MD

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sander -O -i em.mdin -p x.prmtop -c x.inpcrd -o em.mdout -r em.rst         
sander -O -i pr.mdin -p x.prmtop -c em.rst   -o pr.mdout -r pr.rst         
sander -O -i md.mdin -p x.prmtop -c md.rst   -o md.mdout -r md.rst -x md.crd

Analysis

ambpdb -p x.prmtop -c em.rst|crd > em.pdb
vmd
process_mdout.perl
cpptraj
   parm   x.prmtop;  resinfo  atominfo
   trajin  md.crd
       distance
       trajout  md.pdb
   list actions
   run
pbsa