but when I am creating the frcmod file of morinfrom mol2 file this type of error is coming.
>parmchk2 -i morin_opt.mol2 -o morin.frcmod -f mol2
elcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff2
Log file: ./leap.log
Loading parameters: /home/mira/software/amber18/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> loadamberparams morin.frcmod
Loading parameters: ./morin.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadamberprep morin_sybyl_gaff.prepc
Loading Prep file: ./morin_sybyl_gaff.prepc
> savepdb MOL morin.pdb
after packin the protein-organic moleculeand water in packmol I got pdb file and with that file I am running it in leap . then I got the following error.
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff2
----- Source: /home/mira/software/amber18/dat/leap/cmd/leaprc.gaff2
----- Source of /home/mira/software/amber18/dat/leap/cmd/leaprc.gaff2 done
Log file: ./leap.log
Loading parameters: /home/mira/software/amber18/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> source leaprc.protein.ff14SB
----- Source: /home/mira/software/amber18/dat/leap/cmd/leaprc.protein.ff14SB
----- Source of /home/mira/software/amber18/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log
Loading parameters: /home/mira/software/amber18/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/mira/software/amber18/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /home/mira/software/amber18/dat/leap/lib/amino12.lib
Loading library: /home/mira/software/amber18/dat/leap/lib/aminoct12.lib
Loading library: /home/mira/software/amber18/dat/leap/lib/aminont12.lib
> source leaprc.water.tip3p
----- Source: /home/mira/software/amber18/dat/leap/cmd/leaprc.water.tip3p
----- Source of /home/mira/software/amber18/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /home/mira/software/amber18/dat/leap/lib/atomic_ions.lib
Loading library: /home/mira/software/amber18/dat/leap/lib/solvents.lib
Loading parameters: /home/mira/software/amber18/dat/leap/parm/frcmod.tip3p
Reading force field modification type file (frcmod)
Reading title:
This is the additional/replacement parameter set for TIP3P water
Loading parameters: /home/mira/software/amber18/dat/leap/parm/frcmod.ions1lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of monovalent ions for TIP3P water model (12-6 normal usage set)
Loading parameters: /home/mira/software/amber18/dat/leap/parm/frcmod.ionsjc_tip3p
Reading force field modification type file (frcmod)
Reading title:
Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham JPCB (2008)
Loading parameters: /home/mira/software/amber18/dat/leap/parm/frcmod.ions234lm_126_tip3p
Reading force field modification type file (frcmod)
Reading title:
Li/Merz ion parameters of divalent to tetravalent ions for TIP3P water model (12-6 normal usage set)
> loadamberparams morin.frcmod
Loading parameters: ./morin.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadamberprep morin_sybyl_gaff.prepc
Loading Prep file: ./morin_sybyl_gaff.prepc
> x= 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)
total atoms in file: 38525
> saveamberparm x hct.prmtop hct.inpcrd
Checking Unit.
Warning: There is a bond of 27.727215 angstroms between:
Warning: There is a bond of 39.636923 angstroms between:
Warning: There is a bond of 39.843649 angstroms between:
Warning: There is a bond of 46.355835 angstroms between:
Note: Ignoring the warnings from Unit Checking.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Error: Could not find angle parameter: cc - oh - ca
Error: Could not find angle parameter: cc - oh - ca
Error: Could not find angle parameter: cc - oh - ca
Error: Could not find angle parameter: cc - oh - ca
Building proper torsion parameters.
Error: ** No torsion terms for c-cc-oh-ho
Error: ** No torsion terms for c-cc-oh-ca
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for cd-cc-oh-ho
Error: ** No torsion terms for cd-cc-oh-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for ca-os-cd-ca
Error: ** No torsion terms for ca-os-cd-cc
Error: ** No torsion terms for c-cc-oh-ho
Error: ** No torsion terms for c-cc-oh-ca
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for cd-cc-oh-ho
Error: ** No torsion terms for cd-cc-oh-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for ca-os-cd-ca
Error: ** No torsion terms for ca-os-cd-cc
Error: ** No torsion terms for c-cc-oh-ho
Error: ** No torsion terms for c-cc-oh-ca
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for cd-cc-oh-ho
Error: ** No torsion terms for cd-cc-oh-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for ca-os-cd-ca
Error: ** No torsion terms for ca-os-cd-cc
Error: ** No torsion terms for c-cc-oh-ho
Error: ** No torsion terms for c-cc-oh-ca
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for cd-cc-oh-ho
Error: ** No torsion terms for cd-cc-oh-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for ca-os-cd-ca
Error: ** No torsion terms for ca-os-cd-cc
Error: ** No torsion terms for c-cc-oh-ho
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for ca-ca-cd-cc
Error: ** No torsion terms for cd-cc-oh-ho
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for os-cd-ca-ca
Error: ** No torsion terms for ca-os-cd-ca
Error: ** No torsion terms for ca-os-cd-cc
Building improper torsion parameters.
old PREP-specified impropers:
<MOL 171>: C2 C6 C1 O11
<MOL 171>: C1 C5 C6 H9
<MOL 171>: C4 C6 C5 O13
<MOL 171>: C3 C1 C2 H7
<MOL 171>: C2 C4 C3 O25
<MOL 171>: C17 C10 C29 O25
<MOL 171>: C18 C19 C17 C29
<MOL 171>: C17 C20 C18 H30
<MOL 171>: C18 C22 C20 H23
<MOL 171>: C20 C21 C22 O26
<MOL 171>: C22 C19 C21 H24
<MOL 171>: C17 C21 C19 O31
<MOL 171>: C8 C3 C4 C5
<MOL 171>: C4 C10 C8 O28
<MOL 171>: C8 C29 C10 O15
<MOL 172>: C2 C6 C1 O11
<MOL 172>: C1 C5 C6 H9
<MOL 172>: C4 C6 C5 O13
<MOL 172>: C3 C1 C2 H7
<MOL 172>: C2 C4 C3 O25
<MOL 172>: C17 C10 C29 O25
<MOL 172>: C18 C19 C17 C29
<MOL 172>: C17 C20 C18 H30
<MOL 172>: C18 C22 C20 H23
<MOL 172>: C20 C21 C22 O26
<MOL 172>: C22 C19 C21 H24
<MOL 172>: C17 C21 C19 O31
<MOL 172>: C8 C3 C4 C5
<MOL 172>: C4 C10 C8 O28
<MOL 172>: C8 C29 C10 O15
<MOL 173>: C2 C6 C1 O11
<MOL 173>: C1 C5 C6 H9
<MOL 173>: C4 C6 C5 O13
<MOL 173>: C3 C1 C2 H7
<MOL 173>: C2 C4 C3 O25
<MOL 173>: C17 C10 C29 O25
<MOL 173>: C18 C19 C17 C29
<MOL 173>: C17 C20 C18 H30
<MOL 173>: C18 C22 C20 H23
<MOL 173>: C20 C21 C22 O26
<MOL 173>: C22 C19 C21 H24
<MOL 173>: C17 C21 C19 O31
<MOL 173>: C8 C3 C4 C5
<MOL 173>: C4 C10 C8 O28
<MOL 173>: C8 C29 C10 O15
<MOL 174>: C2 C6 C1 O11
<MOL 174>: C1 C5 C6 H9
<MOL 174>: C4 C6 C5 O13
<MOL 174>: C3 C1 C2 H7
<MOL 174>: C2 C4 C3 O25
<MOL 174>: C17 C10 C29 O25
<MOL 174>: C18 C19 C17 C29
<MOL 174>: C17 C20 C18 H30
<MOL 174>: C18 C22 C20 H23
<MOL 174>: C20 C21 C22 O26
<MOL 174>: C22 C19 C21 H24
<MOL 174>: C17 C21 C19 O31
<MOL 174>: C8 C3 C4 C5
<MOL 174>: C4 C10 C8 O28
<MOL 174>: C8 C29 C10 O15
<MOL 175>: C2 C6 C1 O11
<MOL 175>: C1 C5 C6 H9
<MOL 175>: C4 C6 C5 O13
<MOL 175>: C3 C1 C2 H7
<MOL 175>: C2 C4 C3 O25
<MOL 175>: C17 C10 C29 O25
<MOL 175>: C18 C19 C17 C29
<MOL 175>: C17 C20 C18 H30
<MOL 175>: C18 C22 C20 H23
<MOL 175>: C20 C21 C22 O26
<MOL 175>: C22 C19 C21 H24
<MOL 175>: C17 C21 C19 O31
<MOL 175>: C8 C3 C4 C5
<MOL 175>: C4 C10 C8 O28
<MOL 175>: C8 C29 C10 O15
total 545 improper torsions applied
75 improper torsions in old prep form
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Warning: Parameter file was not saved.
________________________________
From: David A Case <david.case.rutgers.edu>
Sent: Tuesday, January 4, 2022 7:34 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] regading no tortion terms
On Tue, Jan 04, 2022, MIRA JHAWAR wrote:
>> loadamberparams morin.frcmod
>Loading parameters: ./morin.frcmod
>
>Error: Could not find angle parameter: cc - oh - ca
First, this angle is not in morin.frcmod, so you should not be surprised
that it is missing.
Second, this angle makes no chemical sense: oh is an oxygen in a hydroxyl
group, so it could never be bonded to two carbon atoms. You need to check
how you created your prep file (I'd recommend using mol2 format rather than
prepc, since you can then visualize the organic molecule easily) and the
corresponding frcmod file.
....good luck....dac
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Received on Sun Jan 09 2022 - 22:30:02 PST
