________________________________
From: MIRA JHAWAR
Sent: Tuesday, January 4, 2022 4:25 PM
To: amber.ambermd.org <amber.ambermd.org>
Subject: regarding no tortion terms
I am trying to get the prmtop file for my preoteina and small organic molecule.But it is showing the following error.
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.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
> savepdb 5hct-5morin-1.pdb
Error: savePdb: Improper number of arguments!
usage: savePdb <object> <filename>
> savepdb x 5hct-5morin-1.pdb
Writing pdb file: 5hct-5morin-1.pdb
> x = loadpdb 5hct-5morin-1.pdb
Loading PDB file: ./5hct-5morin-1.pdb
bond total atoms in file: 38525
> bond x.2.SG x.8.SG
> bond x.36.SG x.42.SG
> bond x.70.SG x.76.SG
> bond x.104.SG x.110.SG
> bond x.138.SG x.144.SG
> savepdb x 5hct-5morin-water.pdb
Writing pdb file: 5hct-5morin-water.pdb
> saveamberparm x 5hct.prmtop 5hct.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.
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jan 04 2022 - 03:30:02 PST
