使用Amber计算单点能三步走

$ tleap
-I: Adding /home/dechin/anaconda3/envs/AmberTools21/dat/leap/prep to search path.
-I: Adding /home/dechin/anaconda3/envs/AmberTools21/dat/leap/lib to search path.
-I: Adding /home/dechin/anaconda3/envs/AmberTools21/dat/leap/parm to search path.
-I: Adding /home/dechin/anaconda3/envs/AmberTools21/dat/leap/cmd to search path.

Welcome to LEaP!
(no leaprc in search path)
> source oldff/leaprc.ff99SB
----- Source: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/cmd/oldff/leaprc.ff99SB
----- Source of /home/dechin/anaconda3/envs/AmberTools21/dat/leap/cmd/oldff/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, Polariz.& LP incl.02/04/99
Loading parameters: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/lib/all_nucleic94.lib
Loading library: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/lib/all_amino94.lib
Loading library: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/lib/all_aminoct94.lib
Loading library: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/lib/all_aminont94.lib
Loading library: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/lib/ions94.lib
Loading library: /home/dechin/anaconda3/envs/AmberTools21/dat/leap/lib/solvents.lib
> pro = loadpdb case2_sponge.pdb
Loading PDB file: ./case2_sponge.pdb
  total atoms in file: 2529
> check pro
Checking 'pro'....
Checking parameters for unit 'pro'.
Checking for bond parameters.
Checking for angle parameters.
check:  Warnings: 652
Unit is OK.
> saveamberparm pro case2_99.prmtop case2_99.inpcrd
Checking Unit.

Warning: There is a bond of 3.346 angstroms between C and N atoms:
-------  .R<TRP 125>.A<C 23> and .R<GLU 126>.A<N 1>

Warning: The unperturbed charge of the unit (1.000000) is not zero.

Note: Ignoring the warnings from Unit Checking.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 497 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 -
   these don't have chain types marked:

        res     total affected

        CALA    1
        NGLU    1
  )
 (no restraints)

energy minimization
 &cntrl
  imin=1,
  ntb=0,
  maxcyc=1,
  cut=9999.0,
 /

$ sander -O -i min.in -o min_99.out -p case2_99.prmtop -c case2_99.inpcrd