dear amber users
we are facing this error and don't know why. may you please help us? the
commands are pasted below.
thank you very much
-I: Adding /share/Application/Amber/amber16/dat/leap/prep to search path.
-I: Adding /share/Application/Amber/amber16/dat/leap/lib to search path.
-I: Adding /share/Application/Amber/amber16/dat/leap/parm to search path.
-I: Adding /share/Application/Amber/amber16/dat/leap/cmd to search path.
Welcome to LEaP! (no leaprc in search path) > source leaprc.protein.ff14SB
----- Source:
/share/Application/Amber/amber16/dat/leap/cmd/leaprc.protein.ff14SB -----
Source of
/share/Application/Amber/amber16/dat/leap/cmd/leaprc.protein.ff14SB done
Log file: ./leap.log Loading parameters:
/share/Application/Amber/amber16/dat/leap/parm/parm10.dat Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA Loading parameters:
/share/Application/Amber/amber16/dat/leap/parm/frcmod.ff14SB Reading force
field modification type file (frcmod) Reading title: ff14SB protein
backbone and sidechain parameters Loading library:
/share/Application/Amber/amber16/dat/leap/lib/amino12.lib Loading library:
/share/Application/Amber/amber16/dat/leap/lib/aminoct12.lib Loading
library: /share/Application/Amber/amber16/dat/leap/lib/aminont12.lib >
source leaprc.water.tip3p ----- Source:
/share/Application/Amber/amber16/dat/leap/cmd/leaprc.water.tip3p -----
Source of /share/Application/Amber/amber16/dat/leap/cmd/leaprc.water.tip3p
done Loading library:
/share/Application/Amber/amber16/dat/leap/lib/atomic_ions.lib Loading
library: /share/Application/Amber/amber16/dat/leap/lib/solvents.lib Loading
parameters:
/share/Application/Amber/amber16/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:
/share/Application/Amber/amber16/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) > source leaprc.GLYCAM_06j-1 ----- Source:
/share/Application/Amber/amber16/dat/leap/cmd/leaprc.GLYCAM_06j-1 -----
Source of /share/Application/Amber/amber16/dat/leap/cmd/leaprc.GLYCAM_06j-1
done Loading parameters:
/share/Application/Amber/amber16/dat/leap/parm/GLYCAM_06j.dat Reading
title: GLYCAM_06_H PARAMETERS (FOR AMBER 11.0, RESP 0.010), COPYRIGHT CCRC
2011 Loading Prep file:
/share/Application/Amber/amber16/dat/leap/prep/GLYCAM_06j-1.prep Loading
library:
/share/Application/Amber/amber16/dat/leap/lib/GLYCAM_amino_06j_12SB .lib
Loading library:
/share/Application/Amber/amber16/dat/leap/lib/GLYCAM_aminoct_06j_12 SB.lib
Loading library:
/share/Application/Amber/amber16/dat/leap/lib/GLYCAM_aminont_06j_12 SB.lib
Substituting map 0HYP -> NHYP for 0HYP -> NHYP Substituting map 1HYP ->
CHYP for 1HYP -> CHYP Loading library:
/share/Application/Amber/amber16/dat/leap/lib/solvents.lib Loading library:
/share/Application/Amber/amber16/dat/leap/lib/atomic_ions.lib Loading
parameters:
/share/Application/Amber/amber16/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) >
gp0= loadpdb structure_AMBER.pdb Loading PDB file: ./structure_AMBER.pdb
total atoms in file: 3369 Leap added 2 missing atoms according to residue
templates: 2 H / lone pairs > saveamberparm gp0 c.prmtop c.inpcrd Checking
Unit. ERROR: The unperturbed charge of the unit: 4.388000 is not integral.
WARNING: The unperturbed charge of the unit: 4.388000 is not zero. --
ignoring the error and warning. Building topology. Building atom
parameters. Building bond parameters. Could not find bond parameter for: OH
- Cg Building angle parameters. Could not find angle parameter: HO - OH -
Cg Could not find angle parameter: OH - Cg - H2 Could not find angle
parameter: OH - Cg - Os Could not find angle parameter: OH - Cg - Cg Could
not find angle parameter: 2C - OH - Cg Building proper torsion parameters.
** No torsion terms for HO-OH-Cg-H2 ** No torsion terms for HO-OH-Cg-Os **
No torsion terms for HO-OH-Cg-Cg ** No torsion terms for OH-Cg-Os-Cg ** No
torsion terms for OH-Cg-Cg-Cg ** No torsion terms for OH-Cg-Cg-H1 ** No
torsion terms for OH-Cg-Cg-Ng ** No torsion terms for H1-2C-OH-Cg ** No
torsion terms for H1-2C-OH-Cg ** No torsion terms for 2C-OH-Cg-H2 ** No
torsion terms for 2C-OH-Cg-Os ** No torsion terms for 2C-OH-Cg-Cg ** No
torsion terms for CX-2C-OH-Cg Building improper torsion parameters. total
708 improper torsions applied Building H-Bond parameters. Incorporating
Non-Bonded adjustments. Parameter file was not saved.
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Received on Mon Nov 15 2021 - 01:30:02 PST
