Now I am doing as you said still I am not getting the parameter files
> antechamber -i morin_opt.mol2 -o morin.mol2
>parmchk2 -i morin.mol2 -o morin.frcmod -f mol2
tleap
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff2
-
> loadamberparams morin.frcmod
Loading parameters: ./morin.frcmod
> MOL = loadmol2 morin.mol2
Loading Mol2 file: ./morin.mol2
Reading MOLECULE named Molecule
> savepdb MOL morin.pdb
Writing pdb file: morin.pdb
> quit
then run the packmol with protein-molecule inp file and get 5hct-5morin.pdb
>tleap
> source leaprc.gaff2
> source leaprc.protein.ff14SB
>source leaprc.water.tip3p
> loadamberparams morin.frcmod
x = loadmol2 morin.mol2
y = loadpdb 5hct-5morin.pdb
Loading PDB file: ./5hct-5morin.pdb
(starting new molecule for chain A)
(starting new molecule for chain B)
(starting new molecule for chain C)
Warning: Unknown residue: MOL number: 170 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: MOL number: 171 type: Nonterminal
Warning: Unknown residue: MOL number: 172 type: Nonterminal
Warning: Unknown residue: MOL number: 173 type: Nonterminal
Warning: Unknown residue: MOL number: 174 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Creating new UNIT for residue: MOL sequence: 171
Created a new atom named: C1 within residue: .R<MOL 171>
Created a new atom named: C2 within residue: .R<MOL 171>
Created a new atom named: C3 within residue: .R<MOL 171>
Created a new atom named: C4 within residue: .R<MOL 171>
Created a new atom named: C5 within residue: .R<MOL 171>
Created a new atom named: C6 within residue: .R<MOL 171>
Created a new atom named: H7 within residue: .R<MOL 171>
Created a new atom named: C8 within residue: .R<MOL 171>
Created a new atom named: H9 within residue: .R<MOL 171>
Created a new atom named: C10 within residue: .R<MOL 171>
Created a new atom named: O11 within residue: .R<MOL 171>
Created a new atom named: H12 within residue: .R<MOL 171>
Created a new atom named: O13 within residue: .R<MOL 171>
Created a new atom named: H14 within residue: .R<MOL 171>
Created a new atom named: O15 within residue: .R<MOL 171>
Created a new atom named: H16 within residue: .R<MOL 171>
Created a new atom named: C17 within residue: .R<MOL 171>
Created a new atom named: C18 within residue: .R<MOL 171>
Created a new atom named: C19 within residue: .R<MOL 171>
Created a new atom named: C20 within residue: .R<MOL 171>
Created a new atom named: C21 within residue: .R<MOL 171>
Created a new atom named: C22 within residue: .R<MOL 171>
Created a new atom named: H23 within residue: .R<MOL 171>
Created a new atom named: H24 within residue: .R<MOL 171>
Created a new atom named: O25 within residue: .R<MOL 171>
Created a new atom named: O26 within residue: .R<MOL 171>
Created a new atom named: H27 within residue: .R<MOL 171>
Created a new atom named: O28 within residue: .R<MOL 171>
Created a new atom named: C29 within residue: .R<MOL 171>
Created a new atom named: H30 within residue: .R<MOL 171>
Created a new atom named: O31 within residue: .R<MOL 171>
Created a new atom named: H32 within residue: .R<MOL 171>
Creating new UNIT for residue: MOL sequence: 172
Created a new atom named: C1 within residue: .R<MOL 172>
Created a new atom named: C2 within residue: .R<MOL 172>
Created a new atom named: C3 within residue: .R<MOL 172>
Created a new atom named: C4 within residue: .R<MOL 172>
Created a new atom named: C5 within residue: .R<MOL 172>
Created a new atom named: C6 within residue: .R<MOL 172>
Created a new atom named: H7 within residue: .R<MOL 172>
Created a new atom named: C8 within residue: .R<MOL 172>
Created a new atom named: H9 within residue: .R<MOL 172>
Created a new atom named: C10 within residue: .R<MOL 172>
Created a new atom named: O11 within residue: .R<MOL 172>
Created a new atom named: H12 within residue: .R<MOL 172>
Created a new atom named: O13 within residue: .R<MOL 172>
Created a new atom named: H14 within residue: .R<MOL 172>
Created a new atom named: O15 within residue: .R<MOL 172>
Created a new atom named: H16 within residue: .R<MOL 172>
Created a new atom named: C17 within residue: .R<MOL 172>
Created a new atom named: C18 within residue: .R<MOL 172>
Created a new atom named: C19 within residue: .R<MOL 172>
Created a new atom named: C20 within residue: .R<MOL 172>
Created a new atom named: C21 within residue: .R<MOL 172>
Created a new atom named: C22 within residue: .R<MOL 172>
Created a new atom named: H23 within residue: .R<MOL 172>
Created a new atom named: H24 within residue: .R<MOL 172>
Created a new atom named: O25 within residue: .R<MOL 172>
Created a new atom named: O26 within residue: .R<MOL 172>
Created a new atom named: H27 within residue: .R<MOL 172>
Created a new atom named: O28 within residue: .R<MOL 172>
Created a new atom named: C29 within residue: .R<MOL 172>
Created a new atom named: H30 within residue: .R<MOL 172>
Created a new atom named: O31 within residue: .R<MOL 172>
Created a new atom named: H32 within residue: .R<MOL 172>
Creating new UNIT for residue: MOL sequence: 173
Created a new atom named: C1 within residue: .R<MOL 173>
Created a new atom named: C2 within residue: .R<MOL 173>
Created a new atom named: C3 within residue: .R<MOL 173>
Created a new atom named: C4 within residue: .R<MOL 173>
Created a new atom named: C5 within residue: .R<MOL 173>
Created a new atom named: C6 within residue: .R<MOL 173>
Created a new atom named: H7 within residue: .R<MOL 173>
Created a new atom named: C8 within residue: .R<MOL 173>
Created a new atom named: H9 within residue: .R<MOL 173>
Created a new atom named: C10 within residue: .R<MOL 173>
Created a new atom named: O11 within residue: .R<MOL 173>
Created a new atom named: H12 within residue: .R<MOL 173>
Created a new atom named: O13 within residue: .R<MOL 173>
Created a new atom named: H14 within residue: .R<MOL 173>
Created a new atom named: O15 within residue: .R<MOL 173>
Created a new atom named: H16 within residue: .R<MOL 173>
Created a new atom named: C17 within residue: .R<MOL 173>
Created a new atom named: C18 within residue: .R<MOL 173>
Created a new atom named: C19 within residue: .R<MOL 173>
Created a new atom named: C20 within residue: .R<MOL 173>
Created a new atom named: C21 within residue: .R<MOL 173>
Created a new atom named: C22 within residue: .R<MOL 173>
Created a new atom named: H23 within residue: .R<MOL 173>
Created a new atom named: H24 within residue: .R<MOL 173>
Created a new atom named: O25 within residue: .R<MOL 173>
Created a new atom named: O26 within residue: .R<MOL 173>
Created a new atom named: H27 within residue: .R<MOL 173>
Created a new atom named: O28 within residue: .R<MOL 173>
Created a new atom named: C29 within residue: .R<MOL 173>
Created a new atom named: H30 within residue: .R<MOL 173>
Created a new atom named: O31 within residue: .R<MOL 173>
Created a new atom named: H32 within residue: .R<MOL 173>
Creating new UNIT for residue: MOL sequence: 174
Created a new atom named: C1 within residue: .R<MOL 174>
Created a new atom named: C2 within residue: .R<MOL 174>
Created a new atom named: C3 within residue: .R<MOL 174>
Created a new atom named: C4 within residue: .R<MOL 174>
Created a new atom named: C5 within residue: .R<MOL 174>
Created a new atom named: C6 within residue: .R<MOL 174>
Created a new atom named: H7 within residue: .R<MOL 174>
Created a new atom named: C8 within residue: .R<MOL 174>
Created a new atom named: H9 within residue: .R<MOL 174>
Created a new atom named: C10 within residue: .R<MOL 174>
Created a new atom named: O11 within residue: .R<MOL 174>
Created a new atom named: H12 within residue: .R<MOL 174>
Created a new atom named: O13 within residue: .R<MOL 174>
Created a new atom named: H14 within residue: .R<MOL 174>
Created a new atom named: O15 within residue: .R<MOL 174>
Created a new atom named: H16 within residue: .R<MOL 174>
Created a new atom named: C17 within residue: .R<MOL 174>
Created a new atom named: C18 within residue: .R<MOL 174>
Created a new atom named: C19 within residue: .R<MOL 174>
Created a new atom named: C20 within residue: .R<MOL 174>
Created a new atom named: C21 within residue: .R<MOL 174>
Created a new atom named: C22 within residue: .R<MOL 174>
Created a new atom named: H23 within residue: .R<MOL 174>
Created a new atom named: H24 within residue: .R<MOL 174>
Created a new atom named: O25 within residue: .R<MOL 174>
Created a new atom named: O26 within residue: .R<MOL 174>
Created a new atom named: H27 within residue: .R<MOL 174>
Created a new atom named: O28 within residue: .R<MOL 174>
Created a new atom named: C29 within residue: .R<MOL 174>
Created a new atom named: H30 within residue: .R<MOL 174>
Created a new atom named: O31 within residue: .R<MOL 174>
Created a new atom named: H32 within residue: .R<MOL 174>
Creating new UNIT for residue: MOL sequence: 175
Created a new atom named: C1 within residue: .R<MOL 175>
Created a new atom named: C2 within residue: .R<MOL 175>
Created a new atom named: C3 within residue: .R<MOL 175>
Created a new atom named: C4 within residue: .R<MOL 175>
Created a new atom named: C5 within residue: .R<MOL 175>
Created a new atom named: C6 within residue: .R<MOL 175>
Created a new atom named: H7 within residue: .R<MOL 175>
Created a new atom named: C8 within residue: .R<MOL 175>
Created a new atom named: H9 within residue: .R<MOL 175>
Created a new atom named: C10 within residue: .R<MOL 175>
Created a new atom named: O11 within residue: .R<MOL 175>
Created a new atom named: H12 within residue: .R<MOL 175>
Created a new atom named: O13 within residue: .R<MOL 175>
Created a new atom named: H14 within residue: .R<MOL 175>
Created a new atom named: O15 within residue: .R<MOL 175>
Created a new atom named: H16 within residue: .R<MOL 175>
Created a new atom named: C17 within residue: .R<MOL 175>
Created a new atom named: C18 within residue: .R<MOL 175>
Created a new atom named: C19 within residue: .R<MOL 175>
Created a new atom named: C20 within residue: .R<MOL 175>
Created a new atom named: C21 within residue: .R<MOL 175>
Created a new atom named: C22 within residue: .R<MOL 175>
Created a new atom named: H23 within residue: .R<MOL 175>
Created a new atom named: H24 within residue: .R<MOL 175>
Created a new atom named: O25 within residue: .R<MOL 175>
Created a new atom named: O26 within residue: .R<MOL 175>
Created a new atom named: H27 within residue: .R<MOL 175>
Created a new atom named: O28 within residue: .R<MOL 175>
Created a new atom named: C29 within residue: .R<MOL 175>
Created a new atom named: H30 within residue: .R<MOL 175>
Created a new atom named: O31 within residue: .R<MOL 175>
Created a new atom named: H32 within residue: .R<MOL 175>
total atoms in file: 38525
The file contained 160 atoms not in residue templates
savepdb y 5hct-5morin-1.pdb
saveamberparm y hct.prmtop hct.inpcrd
Checking Unit.
FATAL: Atom .R<MOL 171>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 171>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 171>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 171>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 171>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 171>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 171>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 171>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 171>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 171>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 171>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 171>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 171>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 171>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 171>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 171>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 171>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 171>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 171>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 171>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 171>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 171>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 171>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 171>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 171>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 171>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 171>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 171>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 171>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 171>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 171>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 171>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 172>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 172>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 172>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 172>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 172>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 172>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 172>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 172>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 172>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 172>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 172>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 172>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 172>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 172>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 172>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 172>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 172>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 172>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 172>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 172>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 172>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 172>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 172>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 172>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 172>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 172>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 172>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 172>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 172>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 172>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 172>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 172>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 173>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 173>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 173>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 173>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 173>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 173>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 173>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 173>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 173>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 173>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 173>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 173>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 173>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 173>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 173>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 173>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 173>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 173>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 173>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 173>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 173>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 173>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 173>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 173>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 173>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 173>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 173>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 173>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 173>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 173>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 173>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 173>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 174>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 174>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 174>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 174>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 174>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 174>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 174>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 174>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 174>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 174>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 174>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 174>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 174>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 174>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 174>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 174>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 174>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 174>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 174>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 174>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 174>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 174>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 174>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 174>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 174>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 174>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 174>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 174>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 174>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 174>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 174>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 174>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 175>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 175>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 175>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 175>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 175>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 175>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 175>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 175>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 175>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 175>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 175>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 175>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 175>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 175>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 175>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 175>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 175>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 175>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 175>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 175>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 175>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 175>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 175>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 175>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 175>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 175>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 175>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 175>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 175>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 175>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 175>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 175>.A<H32 32> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
> quit
Quit
For ypour convinience I am attaching my all files.
Please help me out.
________________________________
From: MIRA JHAWAR <j.mira.iitg.ac.in>
Sent: Tuesday, January 11, 2022 8:54 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] regading no tortion terms
Now I am doing as you said still I am not getting the parameter files
> antechamber -i morin_opt.mol2 -o morin.mol2
>parmchk2 -i morin.mol2 -o morin.frcmod -f mol2
tleap
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff2
-
> loadamberparams morin.frcmod
Loading parameters: ./morin.frcmod
> MOL = loadmol2 morin.mol2
Loading Mol2 file: ./morin.mol2
Reading MOLECULE named Molecule
> savepdb MOL morin.pdb
Writing pdb file: morin.pdb
> quit
then run the packmol with protein-molecule inp file and get 5hct-5morin.pdb
>tleap
> source leaprc.gaff2
> source leaprc.protein.ff14SB
>source leaprc.water.tip3p
> loadamberparams morin.frcmod
x = loadmol2 morin.mol2
y = loadpdb 5hct-5morin.pdb
Loading PDB file: ./5hct-5morin.pdb
(starting new molecule for chain A)
(starting new molecule for chain B)
(starting new molecule for chain C)
Warning: Unknown residue: MOL number: 170 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: MOL number: 171 type: Nonterminal
Warning: Unknown residue: MOL number: 172 type: Nonterminal
Warning: Unknown residue: MOL number: 173 type: Nonterminal
Warning: Unknown residue: MOL number: 174 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Creating new UNIT for residue: MOL sequence: 171
Created a new atom named: C1 within residue: .R<MOL 171>
Created a new atom named: C2 within residue: .R<MOL 171>
Created a new atom named: C3 within residue: .R<MOL 171>
Created a new atom named: C4 within residue: .R<MOL 171>
Created a new atom named: C5 within residue: .R<MOL 171>
Created a new atom named: C6 within residue: .R<MOL 171>
Created a new atom named: H7 within residue: .R<MOL 171>
Created a new atom named: C8 within residue: .R<MOL 171>
Created a new atom named: H9 within residue: .R<MOL 171>
Created a new atom named: C10 within residue: .R<MOL 171>
Created a new atom named: O11 within residue: .R<MOL 171>
Created a new atom named: H12 within residue: .R<MOL 171>
Created a new atom named: O13 within residue: .R<MOL 171>
Created a new atom named: H14 within residue: .R<MOL 171>
Created a new atom named: O15 within residue: .R<MOL 171>
Created a new atom named: H16 within residue: .R<MOL 171>
Created a new atom named: C17 within residue: .R<MOL 171>
Created a new atom named: C18 within residue: .R<MOL 171>
Created a new atom named: C19 within residue: .R<MOL 171>
Created a new atom named: C20 within residue: .R<MOL 171>
Created a new atom named: C21 within residue: .R<MOL 171>
Created a new atom named: C22 within residue: .R<MOL 171>
Created a new atom named: H23 within residue: .R<MOL 171>
Created a new atom named: H24 within residue: .R<MOL 171>
Created a new atom named: O25 within residue: .R<MOL 171>
Created a new atom named: O26 within residue: .R<MOL 171>
Created a new atom named: H27 within residue: .R<MOL 171>
Created a new atom named: O28 within residue: .R<MOL 171>
Created a new atom named: C29 within residue: .R<MOL 171>
Created a new atom named: H30 within residue: .R<MOL 171>
Created a new atom named: O31 within residue: .R<MOL 171>
Created a new atom named: H32 within residue: .R<MOL 171>
Creating new UNIT for residue: MOL sequence: 172
Created a new atom named: C1 within residue: .R<MOL 172>
Created a new atom named: C2 within residue: .R<MOL 172>
Created a new atom named: C3 within residue: .R<MOL 172>
Created a new atom named: C4 within residue: .R<MOL 172>
Created a new atom named: C5 within residue: .R<MOL 172>
Created a new atom named: C6 within residue: .R<MOL 172>
Created a new atom named: H7 within residue: .R<MOL 172>
Created a new atom named: C8 within residue: .R<MOL 172>
Created a new atom named: H9 within residue: .R<MOL 172>
Created a new atom named: C10 within residue: .R<MOL 172>
Created a new atom named: O11 within residue: .R<MOL 172>
Created a new atom named: H12 within residue: .R<MOL 172>
Created a new atom named: O13 within residue: .R<MOL 172>
Created a new atom named: H14 within residue: .R<MOL 172>
Created a new atom named: O15 within residue: .R<MOL 172>
Created a new atom named: H16 within residue: .R<MOL 172>
Created a new atom named: C17 within residue: .R<MOL 172>
Created a new atom named: C18 within residue: .R<MOL 172>
Created a new atom named: C19 within residue: .R<MOL 172>
Created a new atom named: C20 within residue: .R<MOL 172>
Created a new atom named: C21 within residue: .R<MOL 172>
Created a new atom named: C22 within residue: .R<MOL 172>
Created a new atom named: H23 within residue: .R<MOL 172>
Created a new atom named: H24 within residue: .R<MOL 172>
Created a new atom named: O25 within residue: .R<MOL 172>
Created a new atom named: O26 within residue: .R<MOL 172>
Created a new atom named: H27 within residue: .R<MOL 172>
Created a new atom named: O28 within residue: .R<MOL 172>
Created a new atom named: C29 within residue: .R<MOL 172>
Created a new atom named: H30 within residue: .R<MOL 172>
Created a new atom named: O31 within residue: .R<MOL 172>
Created a new atom named: H32 within residue: .R<MOL 172>
Creating new UNIT for residue: MOL sequence: 173
Created a new atom named: C1 within residue: .R<MOL 173>
Created a new atom named: C2 within residue: .R<MOL 173>
Created a new atom named: C3 within residue: .R<MOL 173>
Created a new atom named: C4 within residue: .R<MOL 173>
Created a new atom named: C5 within residue: .R<MOL 173>
Created a new atom named: C6 within residue: .R<MOL 173>
Created a new atom named: H7 within residue: .R<MOL 173>
Created a new atom named: C8 within residue: .R<MOL 173>
Created a new atom named: H9 within residue: .R<MOL 173>
Created a new atom named: C10 within residue: .R<MOL 173>
Created a new atom named: O11 within residue: .R<MOL 173>
Created a new atom named: H12 within residue: .R<MOL 173>
Created a new atom named: O13 within residue: .R<MOL 173>
Created a new atom named: H14 within residue: .R<MOL 173>
Created a new atom named: O15 within residue: .R<MOL 173>
Created a new atom named: H16 within residue: .R<MOL 173>
Created a new atom named: C17 within residue: .R<MOL 173>
Created a new atom named: C18 within residue: .R<MOL 173>
Created a new atom named: C19 within residue: .R<MOL 173>
Created a new atom named: C20 within residue: .R<MOL 173>
Created a new atom named: C21 within residue: .R<MOL 173>
Created a new atom named: C22 within residue: .R<MOL 173>
Created a new atom named: H23 within residue: .R<MOL 173>
Created a new atom named: H24 within residue: .R<MOL 173>
Created a new atom named: O25 within residue: .R<MOL 173>
Created a new atom named: O26 within residue: .R<MOL 173>
Created a new atom named: H27 within residue: .R<MOL 173>
Created a new atom named: O28 within residue: .R<MOL 173>
Created a new atom named: C29 within residue: .R<MOL 173>
Created a new atom named: H30 within residue: .R<MOL 173>
Created a new atom named: O31 within residue: .R<MOL 173>
Created a new atom named: H32 within residue: .R<MOL 173>
Creating new UNIT for residue: MOL sequence: 174
Created a new atom named: C1 within residue: .R<MOL 174>
Created a new atom named: C2 within residue: .R<MOL 174>
Created a new atom named: C3 within residue: .R<MOL 174>
Created a new atom named: C4 within residue: .R<MOL 174>
Created a new atom named: C5 within residue: .R<MOL 174>
Created a new atom named: C6 within residue: .R<MOL 174>
Created a new atom named: H7 within residue: .R<MOL 174>
Created a new atom named: C8 within residue: .R<MOL 174>
Created a new atom named: H9 within residue: .R<MOL 174>
Created a new atom named: C10 within residue: .R<MOL 174>
Created a new atom named: O11 within residue: .R<MOL 174>
Created a new atom named: H12 within residue: .R<MOL 174>
Created a new atom named: O13 within residue: .R<MOL 174>
Created a new atom named: H14 within residue: .R<MOL 174>
Created a new atom named: O15 within residue: .R<MOL 174>
Created a new atom named: H16 within residue: .R<MOL 174>
Created a new atom named: C17 within residue: .R<MOL 174>
Created a new atom named: C18 within residue: .R<MOL 174>
Created a new atom named: C19 within residue: .R<MOL 174>
Created a new atom named: C20 within residue: .R<MOL 174>
Created a new atom named: C21 within residue: .R<MOL 174>
Created a new atom named: C22 within residue: .R<MOL 174>
Created a new atom named: H23 within residue: .R<MOL 174>
Created a new atom named: H24 within residue: .R<MOL 174>
Created a new atom named: O25 within residue: .R<MOL 174>
Created a new atom named: O26 within residue: .R<MOL 174>
Created a new atom named: H27 within residue: .R<MOL 174>
Created a new atom named: O28 within residue: .R<MOL 174>
Created a new atom named: C29 within residue: .R<MOL 174>
Created a new atom named: H30 within residue: .R<MOL 174>
Created a new atom named: O31 within residue: .R<MOL 174>
Created a new atom named: H32 within residue: .R<MOL 174>
Creating new UNIT for residue: MOL sequence: 175
Created a new atom named: C1 within residue: .R<MOL 175>
Created a new atom named: C2 within residue: .R<MOL 175>
Created a new atom named: C3 within residue: .R<MOL 175>
Created a new atom named: C4 within residue: .R<MOL 175>
Created a new atom named: C5 within residue: .R<MOL 175>
Created a new atom named: C6 within residue: .R<MOL 175>
Created a new atom named: H7 within residue: .R<MOL 175>
Created a new atom named: C8 within residue: .R<MOL 175>
Created a new atom named: H9 within residue: .R<MOL 175>
Created a new atom named: C10 within residue: .R<MOL 175>
Created a new atom named: O11 within residue: .R<MOL 175>
Created a new atom named: H12 within residue: .R<MOL 175>
Created a new atom named: O13 within residue: .R<MOL 175>
Created a new atom named: H14 within residue: .R<MOL 175>
Created a new atom named: O15 within residue: .R<MOL 175>
Created a new atom named: H16 within residue: .R<MOL 175>
Created a new atom named: C17 within residue: .R<MOL 175>
Created a new atom named: C18 within residue: .R<MOL 175>
Created a new atom named: C19 within residue: .R<MOL 175>
Created a new atom named: C20 within residue: .R<MOL 175>
Created a new atom named: C21 within residue: .R<MOL 175>
Created a new atom named: C22 within residue: .R<MOL 175>
Created a new atom named: H23 within residue: .R<MOL 175>
Created a new atom named: H24 within residue: .R<MOL 175>
Created a new atom named: O25 within residue: .R<MOL 175>
Created a new atom named: O26 within residue: .R<MOL 175>
Created a new atom named: H27 within residue: .R<MOL 175>
Created a new atom named: O28 within residue: .R<MOL 175>
Created a new atom named: C29 within residue: .R<MOL 175>
Created a new atom named: H30 within residue: .R<MOL 175>
Created a new atom named: O31 within residue: .R<MOL 175>
Created a new atom named: H32 within residue: .R<MOL 175>
total atoms in file: 38525
The file contained 160 atoms not in residue templates
savepdb y 5hct-5morin-1.pdb
saveamberparm y hct.prmtop hct.inpcrd
Checking Unit.
FATAL: Atom .R<MOL 171>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 171>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 171>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 171>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 171>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 171>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 171>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 171>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 171>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 171>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 171>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 171>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 171>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 171>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 171>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 171>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 171>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 171>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 171>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 171>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 171>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 171>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 171>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 171>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 171>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 171>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 171>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 171>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 171>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 171>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 171>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 171>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 172>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 172>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 172>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 172>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 172>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 172>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 172>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 172>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 172>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 172>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 172>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 172>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 172>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 172>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 172>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 172>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 172>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 172>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 172>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 172>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 172>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 172>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 172>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 172>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 172>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 172>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 172>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 172>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 172>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 172>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 172>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 172>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 173>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 173>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 173>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 173>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 173>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 173>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 173>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 173>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 173>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 173>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 173>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 173>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 173>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 173>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 173>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 173>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 173>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 173>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 173>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 173>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 173>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 173>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 173>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 173>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 173>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 173>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 173>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 173>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 173>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 173>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 173>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 173>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 174>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 174>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 174>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 174>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 174>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 174>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 174>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 174>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 174>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 174>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 174>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 174>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 174>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 174>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 174>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 174>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 174>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 174>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 174>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 174>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 174>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 174>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 174>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 174>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 174>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 174>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 174>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 174>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 174>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 174>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 174>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 174>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 175>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 175>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 175>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 175>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 175>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 175>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 175>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 175>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 175>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 175>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 175>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 175>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 175>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 175>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 175>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 175>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 175>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 175>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 175>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 175>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 175>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 175>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 175>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 175>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 175>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 175>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 175>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 175>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 175>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 175>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 175>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 175>.A<H32 32> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
> quit
Quit
For ypour convinience I am attaching my all files.
Please help me out.
________________________________
From: MIRA JHAWAR <j.mira.iitg.ac.in>
Sent: Tuesday, January 11, 2022 8:48 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] regading no tortion terms
Now I am doing as you said still I am not getting the parameter files
> antechamber -i morin_opt.mol2 -o morin.mol2
>parmchk2 -i morin.mol2 -o morin.frcmod -f mol2
tleap
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff2
-
> loadamberparams morin.frcmod
Loading parameters: ./morin.frcmod
> MOL = loadmol2 morin.mol2
Loading Mol2 file: ./morin.mol2
Reading MOLECULE named Molecule
> savepdb MOL morin.pdb
Writing pdb file: morin.pdb
> quit
then run the packmol with protein-molecule inp file and get 5hct-5morin.pdb
>tleap
> source leaprc.gaff2
> source leaprc.protein.ff14SB
>source leaprc.water.tip3p
> loadamberparams morin.frcmod
x = loadmol2 morin.mol2
y = loadpdb 5hct-5morin.pdb
Loading PDB file: ./5hct-5morin.pdb
(starting new molecule for chain A)
(starting new molecule for chain B)
(starting new molecule for chain C)
Warning: Unknown residue: MOL number: 170 type: Terminal/beginning
..relaxing end constraints to try for a dbase match
Warning: -no luck
Warning: Unknown residue: MOL number: 171 type: Nonterminal
Warning: Unknown residue: MOL number: 172 type: Nonterminal
Warning: Unknown residue: MOL number: 173 type: Nonterminal
Warning: Unknown residue: MOL number: 174 type: Terminal/last
..relaxing end constraints to try for a dbase match
Warning: -no luck
Creating new UNIT for residue: MOL sequence: 171
Created a new atom named: C1 within residue: .R<MOL 171>
Created a new atom named: C2 within residue: .R<MOL 171>
Created a new atom named: C3 within residue: .R<MOL 171>
Created a new atom named: C4 within residue: .R<MOL 171>
Created a new atom named: C5 within residue: .R<MOL 171>
Created a new atom named: C6 within residue: .R<MOL 171>
Created a new atom named: H7 within residue: .R<MOL 171>
Created a new atom named: C8 within residue: .R<MOL 171>
Created a new atom named: H9 within residue: .R<MOL 171>
Created a new atom named: C10 within residue: .R<MOL 171>
Created a new atom named: O11 within residue: .R<MOL 171>
Created a new atom named: H12 within residue: .R<MOL 171>
Created a new atom named: O13 within residue: .R<MOL 171>
Created a new atom named: H14 within residue: .R<MOL 171>
Created a new atom named: O15 within residue: .R<MOL 171>
Created a new atom named: H16 within residue: .R<MOL 171>
Created a new atom named: C17 within residue: .R<MOL 171>
Created a new atom named: C18 within residue: .R<MOL 171>
Created a new atom named: C19 within residue: .R<MOL 171>
Created a new atom named: C20 within residue: .R<MOL 171>
Created a new atom named: C21 within residue: .R<MOL 171>
Created a new atom named: C22 within residue: .R<MOL 171>
Created a new atom named: H23 within residue: .R<MOL 171>
Created a new atom named: H24 within residue: .R<MOL 171>
Created a new atom named: O25 within residue: .R<MOL 171>
Created a new atom named: O26 within residue: .R<MOL 171>
Created a new atom named: H27 within residue: .R<MOL 171>
Created a new atom named: O28 within residue: .R<MOL 171>
Created a new atom named: C29 within residue: .R<MOL 171>
Created a new atom named: H30 within residue: .R<MOL 171>
Created a new atom named: O31 within residue: .R<MOL 171>
Created a new atom named: H32 within residue: .R<MOL 171>
Creating new UNIT for residue: MOL sequence: 172
Created a new atom named: C1 within residue: .R<MOL 172>
Created a new atom named: C2 within residue: .R<MOL 172>
Created a new atom named: C3 within residue: .R<MOL 172>
Created a new atom named: C4 within residue: .R<MOL 172>
Created a new atom named: C5 within residue: .R<MOL 172>
Created a new atom named: C6 within residue: .R<MOL 172>
Created a new atom named: H7 within residue: .R<MOL 172>
Created a new atom named: C8 within residue: .R<MOL 172>
Created a new atom named: H9 within residue: .R<MOL 172>
Created a new atom named: C10 within residue: .R<MOL 172>
Created a new atom named: O11 within residue: .R<MOL 172>
Created a new atom named: H12 within residue: .R<MOL 172>
Created a new atom named: O13 within residue: .R<MOL 172>
Created a new atom named: H14 within residue: .R<MOL 172>
Created a new atom named: O15 within residue: .R<MOL 172>
Created a new atom named: H16 within residue: .R<MOL 172>
Created a new atom named: C17 within residue: .R<MOL 172>
Created a new atom named: C18 within residue: .R<MOL 172>
Created a new atom named: C19 within residue: .R<MOL 172>
Created a new atom named: C20 within residue: .R<MOL 172>
Created a new atom named: C21 within residue: .R<MOL 172>
Created a new atom named: C22 within residue: .R<MOL 172>
Created a new atom named: H23 within residue: .R<MOL 172>
Created a new atom named: H24 within residue: .R<MOL 172>
Created a new atom named: O25 within residue: .R<MOL 172>
Created a new atom named: O26 within residue: .R<MOL 172>
Created a new atom named: H27 within residue: .R<MOL 172>
Created a new atom named: O28 within residue: .R<MOL 172>
Created a new atom named: C29 within residue: .R<MOL 172>
Created a new atom named: H30 within residue: .R<MOL 172>
Created a new atom named: O31 within residue: .R<MOL 172>
Created a new atom named: H32 within residue: .R<MOL 172>
Creating new UNIT for residue: MOL sequence: 173
Created a new atom named: C1 within residue: .R<MOL 173>
Created a new atom named: C2 within residue: .R<MOL 173>
Created a new atom named: C3 within residue: .R<MOL 173>
Created a new atom named: C4 within residue: .R<MOL 173>
Created a new atom named: C5 within residue: .R<MOL 173>
Created a new atom named: C6 within residue: .R<MOL 173>
Created a new atom named: H7 within residue: .R<MOL 173>
Created a new atom named: C8 within residue: .R<MOL 173>
Created a new atom named: H9 within residue: .R<MOL 173>
Created a new atom named: C10 within residue: .R<MOL 173>
Created a new atom named: O11 within residue: .R<MOL 173>
Created a new atom named: H12 within residue: .R<MOL 173>
Created a new atom named: O13 within residue: .R<MOL 173>
Created a new atom named: H14 within residue: .R<MOL 173>
Created a new atom named: O15 within residue: .R<MOL 173>
Created a new atom named: H16 within residue: .R<MOL 173>
Created a new atom named: C17 within residue: .R<MOL 173>
Created a new atom named: C18 within residue: .R<MOL 173>
Created a new atom named: C19 within residue: .R<MOL 173>
Created a new atom named: C20 within residue: .R<MOL 173>
Created a new atom named: C21 within residue: .R<MOL 173>
Created a new atom named: C22 within residue: .R<MOL 173>
Created a new atom named: H23 within residue: .R<MOL 173>
Created a new atom named: H24 within residue: .R<MOL 173>
Created a new atom named: O25 within residue: .R<MOL 173>
Created a new atom named: O26 within residue: .R<MOL 173>
Created a new atom named: H27 within residue: .R<MOL 173>
Created a new atom named: O28 within residue: .R<MOL 173>
Created a new atom named: C29 within residue: .R<MOL 173>
Created a new atom named: H30 within residue: .R<MOL 173>
Created a new atom named: O31 within residue: .R<MOL 173>
Created a new atom named: H32 within residue: .R<MOL 173>
Creating new UNIT for residue: MOL sequence: 174
Created a new atom named: C1 within residue: .R<MOL 174>
Created a new atom named: C2 within residue: .R<MOL 174>
Created a new atom named: C3 within residue: .R<MOL 174>
Created a new atom named: C4 within residue: .R<MOL 174>
Created a new atom named: C5 within residue: .R<MOL 174>
Created a new atom named: C6 within residue: .R<MOL 174>
Created a new atom named: H7 within residue: .R<MOL 174>
Created a new atom named: C8 within residue: .R<MOL 174>
Created a new atom named: H9 within residue: .R<MOL 174>
Created a new atom named: C10 within residue: .R<MOL 174>
Created a new atom named: O11 within residue: .R<MOL 174>
Created a new atom named: H12 within residue: .R<MOL 174>
Created a new atom named: O13 within residue: .R<MOL 174>
Created a new atom named: H14 within residue: .R<MOL 174>
Created a new atom named: O15 within residue: .R<MOL 174>
Created a new atom named: H16 within residue: .R<MOL 174>
Created a new atom named: C17 within residue: .R<MOL 174>
Created a new atom named: C18 within residue: .R<MOL 174>
Created a new atom named: C19 within residue: .R<MOL 174>
Created a new atom named: C20 within residue: .R<MOL 174>
Created a new atom named: C21 within residue: .R<MOL 174>
Created a new atom named: C22 within residue: .R<MOL 174>
Created a new atom named: H23 within residue: .R<MOL 174>
Created a new atom named: H24 within residue: .R<MOL 174>
Created a new atom named: O25 within residue: .R<MOL 174>
Created a new atom named: O26 within residue: .R<MOL 174>
Created a new atom named: H27 within residue: .R<MOL 174>
Created a new atom named: O28 within residue: .R<MOL 174>
Created a new atom named: C29 within residue: .R<MOL 174>
Created a new atom named: H30 within residue: .R<MOL 174>
Created a new atom named: O31 within residue: .R<MOL 174>
Created a new atom named: H32 within residue: .R<MOL 174>
Creating new UNIT for residue: MOL sequence: 175
Created a new atom named: C1 within residue: .R<MOL 175>
Created a new atom named: C2 within residue: .R<MOL 175>
Created a new atom named: C3 within residue: .R<MOL 175>
Created a new atom named: C4 within residue: .R<MOL 175>
Created a new atom named: C5 within residue: .R<MOL 175>
Created a new atom named: C6 within residue: .R<MOL 175>
Created a new atom named: H7 within residue: .R<MOL 175>
Created a new atom named: C8 within residue: .R<MOL 175>
Created a new atom named: H9 within residue: .R<MOL 175>
Created a new atom named: C10 within residue: .R<MOL 175>
Created a new atom named: O11 within residue: .R<MOL 175>
Created a new atom named: H12 within residue: .R<MOL 175>
Created a new atom named: O13 within residue: .R<MOL 175>
Created a new atom named: H14 within residue: .R<MOL 175>
Created a new atom named: O15 within residue: .R<MOL 175>
Created a new atom named: H16 within residue: .R<MOL 175>
Created a new atom named: C17 within residue: .R<MOL 175>
Created a new atom named: C18 within residue: .R<MOL 175>
Created a new atom named: C19 within residue: .R<MOL 175>
Created a new atom named: C20 within residue: .R<MOL 175>
Created a new atom named: C21 within residue: .R<MOL 175>
Created a new atom named: C22 within residue: .R<MOL 175>
Created a new atom named: H23 within residue: .R<MOL 175>
Created a new atom named: H24 within residue: .R<MOL 175>
Created a new atom named: O25 within residue: .R<MOL 175>
Created a new atom named: O26 within residue: .R<MOL 175>
Created a new atom named: H27 within residue: .R<MOL 175>
Created a new atom named: O28 within residue: .R<MOL 175>
Created a new atom named: C29 within residue: .R<MOL 175>
Created a new atom named: H30 within residue: .R<MOL 175>
Created a new atom named: O31 within residue: .R<MOL 175>
Created a new atom named: H32 within residue: .R<MOL 175>
total atoms in file: 38525
The file contained 160 atoms not in residue templates
savepdb y 5hct-5morin-1.pdb
saveamberparm y hct.prmtop hct.inpcrd
Checking Unit.
FATAL: Atom .R<MOL 171>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 171>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 171>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 171>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 171>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 171>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 171>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 171>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 171>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 171>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 171>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 171>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 171>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 171>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 171>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 171>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 171>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 171>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 171>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 171>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 171>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 171>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 171>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 171>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 171>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 171>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 171>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 171>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 171>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 171>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 171>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 171>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 172>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 172>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 172>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 172>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 172>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 172>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 172>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 172>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 172>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 172>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 172>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 172>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 172>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 172>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 172>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 172>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 172>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 172>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 172>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 172>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 172>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 172>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 172>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 172>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 172>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 172>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 172>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 172>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 172>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 172>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 172>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 172>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 173>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 173>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 173>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 173>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 173>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 173>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 173>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 173>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 173>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 173>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 173>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 173>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 173>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 173>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 173>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 173>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 173>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 173>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 173>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 173>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 173>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 173>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 173>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 173>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 173>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 173>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 173>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 173>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 173>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 173>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 173>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 173>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 174>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 174>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 174>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 174>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 174>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 174>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 174>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 174>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 174>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 174>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 174>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 174>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 174>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 174>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 174>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 174>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 174>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 174>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 174>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 174>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 174>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 174>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 174>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 174>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 174>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 174>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 174>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 174>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 174>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 174>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 174>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 174>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 175>.A<C1 1> does not have a type.
FATAL: Atom .R<MOL 175>.A<C2 2> does not have a type.
FATAL: Atom .R<MOL 175>.A<C3 3> does not have a type.
FATAL: Atom .R<MOL 175>.A<C4 4> does not have a type.
FATAL: Atom .R<MOL 175>.A<C5 5> does not have a type.
FATAL: Atom .R<MOL 175>.A<C6 6> does not have a type.
FATAL: Atom .R<MOL 175>.A<H7 7> does not have a type.
FATAL: Atom .R<MOL 175>.A<C8 8> does not have a type.
FATAL: Atom .R<MOL 175>.A<H9 9> does not have a type.
FATAL: Atom .R<MOL 175>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 175>.A<O11 11> does not have a type.
FATAL: Atom .R<MOL 175>.A<H12 12> does not have a type.
FATAL: Atom .R<MOL 175>.A<O13 13> does not have a type.
FATAL: Atom .R<MOL 175>.A<H14 14> does not have a type.
FATAL: Atom .R<MOL 175>.A<O15 15> does not have a type.
FATAL: Atom .R<MOL 175>.A<H16 16> does not have a type.
FATAL: Atom .R<MOL 175>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 175>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 175>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 175>.A<C20 20> does not have a type.
FATAL: Atom .R<MOL 175>.A<C21 21> does not have a type.
FATAL: Atom .R<MOL 175>.A<C22 22> does not have a type.
FATAL: Atom .R<MOL 175>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 175>.A<H24 24> does not have a type.
FATAL: Atom .R<MOL 175>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 175>.A<O26 26> does not have a type.
FATAL: Atom .R<MOL 175>.A<H27 27> does not have a type.
FATAL: Atom .R<MOL 175>.A<O28 28> does not have a type.
FATAL: Atom .R<MOL 175>.A<C29 29> does not have a type.
FATAL: Atom .R<MOL 175>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 175>.A<O31 31> does not have a type.
FATAL: Atom .R<MOL 175>.A<H32 32> does not have a type.
Error: Failed to generate parameters
Warning: Parameter file was not saved.
> quit
Quit
For ypour convinience I am attaching my all files.
Please help me out.
________________________________
From: MIRA JHAWAR <j.mira.iitg.ac.in>
Sent: Tuesday, January 11, 2022 7:50 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] regading no tortion terms
I am using fresh directory with freah files though I am getting errors
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________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, January 11, 2022 7:45:37 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] regading no tortion terms
On Mon, Jan 10, 2022, MIRA JHAWAR wrote:
>Error: Could not find angle parameter: cc - oh - ca
Anselm is correct: this problem was discussed in my earlier email.
> i have done the following things-
> antechamber -i morin_opt.mol2 -o morin.mol2
> parmchk2 -i morin.mol2 -o morin.frcmod
Your antechamber run will need to add a method to assign charges.
I'd suggest really starting from the beginning. Don't use the prepc file
you have. Don't load files like "morin-1.frcmod", unless you are sure you
know where they came from. Consider starting in a fresh directory, so there
is no chance that you will accidentally use the older files.
....good luck....dac
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Received on Tue Jan 11 2022 - 08:00:02 PST
