Mira,
your atom type assignment in your ligand seems to be wrong, as was
pointed out already by David. It is defined in the prepc file you load
into leap.
Thus, have a look into that file, check the atom types therein (have a
look into the gaff paper or into the gaff2.dat file, where the atom
types are also shortly described) and correct wrong assignments.
Good luck.
Anselm
Bioinformatik | NHR.FAU
Friedrich-Alexander-Universität Erlangen-Nürnberg
Germany
Am 10.01.2022 um 13:08 schrieb MIRA JHAWAR:
>
> ________________________________
> From: MIRA JHAWAR <j.mira.iitg.ac.in>
> Sent: Monday, January 10, 2022 11:38 AM
> To: AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] regading no tortion terms
>
> 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
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Jan 10 2022 - 06:30:03 PST
