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________________________________
From: MIRA JHAWAR <j.mira.iitg.ac.in>
Sent: Monday, January 10, 2022 9:33:14 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] regading no tortion terms
i have done the following things-
antechamber -i morin_opt.mol2 -o morin.mol2
> parmchk2 -i morin.mol2 -o morin.frcmod
tleap
Welcome to LEaP!
(no leaprc in search path)
> source leaprc.gaff2
----- Source: /home/mira/software/amber18/dat/leap/cmd/leaprc.gaff
----- Source of /home/mira/software/amber18/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /home/mira/software/amber18/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
> loadamberparams morin-1.frcmod
Loading parameters: ./morin-1.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> x = loadmol2 morin.mol2
Loading Mol2 file: ./morin.mol2
Reading MOLECULE named Molecule
> savepdb MOl morin.pdb
> savepdb x morin.pdb
Writing pdb file: morin.pdb
>
packmol < 5hct-5morin.inp and get 5hct-5morin.pdb
tleap
-I: Adding /home/mira/software/amber18/dat/leap/prep to search path.
-I: Adding /home/mira/software/amber18/dat/leap/lib to search path.
-I: Adding /home/mira/software/amber18/dat/leap/parm to search path.
-I: Adding /home/mira/software/amber18/dat/leap/cmd to search path.
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-1.frcmod
Loading parameters: ./morin-1.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> loadamaberprep morin_sybyl_gaff.prepc
Error: Error from the parser: syntax error
> loadamberprep morin_sybyl_gaff.prepc
Loading Prep file: ./morin_sybyl_gaff.prepc
> x = loadmol2 morin.mol2
Loading Mol2 file: ./morin.mol2
Reading MOLECULE named Molecule
> 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)
total atoms in file: 38525
> savepdb y 5hct-5morin-1.pdb
Writing pdb file: 5hct-5morin-1.pdb
> saveamberparm y 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-ca
Error: ** No torsion terms for cd-cc-oh-ca
Error: ** No torsion terms for c-cc-oh-ca
Error: ** No torsion terms for cd-cc-oh-ca
Error: ** No torsion terms for c-cc-oh-ca
Error: ** No torsion terms for cd-cc-oh-ca
Error: ** No torsion terms for c-cc-oh-ca
Error: ** No torsion terms for cd-cc-oh-ca
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 594 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: Monday, January 10, 2022 7:44 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] regading no tortion terms
On Mon, Jan 10, 2022, MIRA JHAWAR wrote:
>these are my mol2 file of organic molecule and frcmod file
Your mol2 file, and (presumably) the ./morin_sybyl_gaff.prepc that you are
actually using for your tleap runs, don't have gaff2 atom types. Did you
actually run antechamber, and not just parmchk2?
I have to guess here a lot about what you did, but here's what it looks
like: You did a Gaussian geometry optimization, got a mol2 file from
Gaussview, and tried to feed that to parmchk2. This won't work. You need
to start with the GaussView mol2 file, go through antechamber to get a mol2
file with gaff atom types. Then feed that into parmchk2.
If the "morin_sybyl_gaff.prepc" indeed has Sybyl atom types (as its name
suggests), it is not of much use for anything related to Amber.
And the frcmod file you have is also badly flawed; I'd delete it so you
won't accidentally use it later.
Don't neglect to investigate the long bond lengths reported by tleap.
Apologies if I my guess about what you did is wrong.
...dac
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Received on Tue Jan 11 2022 - 04:30:02 PST
