Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./tleap.in
----- Source: /usr/local/amber20/dat/leap/cmd/leaprc.gaff
----- Source of /usr/local/amber20/dat/leap/cmd/leaprc.gaff done
Log file: ./leap.log
Loading parameters: /usr/local/amber20/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.81, May 2017)
----- Source: /usr/local/amber20/dat/leap/cmd/leaprc.water.tip3p
----- Source of /usr/local/amber20/dat/leap/cmd/leaprc.water.tip3p done
Loading library: /usr/local/amber20/dat/leap/lib/atomic_ions.lib
Loading library: /usr/local/amber20/dat/leap/lib/solvents.lib
Loading parameters: /usr/local/amber20/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: /usr/local/amber20/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: /usr/local/amber20/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: /usr/local/amber20/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)
Loading library: /usr/local/amber20/dat/leap/lib/solvents.lib
Loading parameters: ./frcmod.meoh
Reading force field modification type file (frcmod)
Reading title:
vdw meoh
Loading Prep file: ./MOH.prepi
/usr/local/amber20/bin/teLeap: Warning!
1 of 9 atoms missing charges on atoms lines: methanol
Loading PDB file: ./MOH.pdb
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-C1-O1-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 2
Leap added 4 missing atoms according to residue templates:
4 H / lone pairs
Solute vdw bounding box: 5.045 3.851 3.816
Total bounding box for atom centers: 25.045 23.851 23.816
Solvent unit box: 18.774 18.774 18.774
Total vdw box size: 27.968 27.188 26.933 angstroms.
Volume: 20480.043 A^3
Mass > 7325.480 amu, Density > 0.594 g/cc
(type - hence mass - of one or more atoms could not be found)
Added 405 residues.
Writing pdb file: methanol_solvated.pdb
printing CRYST1 record to PDB file with box info
Checking Unit.
Building topology.
Building atom parameters.
/usr/local/amber20/bin/teLeap: Error!
For atom (.R<MOH 1>.A<HC1 1>) could not find vdW (or other) parameters for type (H1)
/usr/local/amber20/bin/teLeap: Error!
For atom (.R<MOH 1>.A<HC2 3>) could not find vdW (or other) parameters for type (H1)
/usr/local/amber20/bin/teLeap: Error!
For atom (.R<MOH 1>.A<HC3 4>) could not find vdW (or other) parameters for type (H1)
/usr/local/amber20/bin/teLeap: Warning!
Parameter file was not saved.
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Received on Mon Feb 07 2022 - 10:00:03 PST
