log started: Wed Mar 26 10:37:10 2025

Log file: ./leap.log
>> #
>> # ----- leaprc for loading the general Amber Force field.
>> #       This file is mostly for use with Antechamber
>> #
>> #	load atom type hybridizations
>> #
>> addAtomTypes {
>> 	{ "h1"  "H" "sp3" }
>> 	{ "h2"  "H" "sp3" }
>> 	{ "h3"  "H" "sp3" }
>> 	{ "h4"  "H" "sp3" }
>> 	{ "h5"  "H" "sp3" }
>> 	{ "ha"  "H" "sp3" }
>> 	{ "hc"  "H" "sp3" }
>> 	{ "hn"  "H" "sp3" }
>> 	{ "ho"  "H" "sp3" }
>> 	{ "hp"  "H" "sp3" }
>> 	{ "hs"  "H" "sp3" }
>> 	{ "hw"  "H" "sp3" }
>> 	{ "hx"  "H" "sp3" }
>> 	{ "o"  "O" "sp2" }
>> 	{ "o2"  "O" "sp2" }
>> 	{ "oh"  "O" "sp3" }
>> 	{ "op"  "O" "sp3" }
>> 	{ "oq"  "O" "sp3" }
>> 	{ "os"  "O" "sp3" }
>> 	{ "ow"  "O" "sp3" }
>> 	{ "c"  "C" "sp2" }
>> 	{ "c1"  "C" "sp2" }
>> 	{ "c2"  "C" "sp2" }
>> 	{ "c3"  "C" "sp3" }
>> 	{ "ca"  "C" "sp2" }
>> 	{ "cc"  "C" "sp2" }
>> 	{ "cd"  "C" "sp2" }
>> 	{ "ce"  "C" "sp2" }
>> 	{ "cf"  "C" "sp2" }
>> 	{ "cg"  "C" "sp2" }
>> 	{ "ch"  "C" "sp2" }
>> 	{ "cp"  "C" "sp2" }
>> 	{ "cs"  "C" "sp2" }
>> 	{ "cq"  "C" "sp2" }
>> 	{ "cu"  "C" "sp2" }
>> 	{ "cv"  "C" "sp2" }
>> 	{ "cx"  "C" "sp2" }
>> 	{ "cy"  "C" "sp2" }
>> 	{ "cz"  "C" "sp2" }
>> 	{ "n"   "N" "sp2" }
>> 	{ "n1"  "N" "sp2" }
>> 	{ "n2"  "N" "sp2" }
>> 	{ "n3"  "N" "sp3" }
>> 	{ "n4"  "N" "sp3" }
>> 	{ "n5"  "N" "sp3" }
>> 	{ "n6"  "N" "sp3" }
>> 	{ "n7"  "N" "sp3" }
>> 	{ "n8"  "N" "sp3" }
>> 	{ "n9"  "N" "sp3" }
>> 	{ "na"  "N" "sp2" }
>> 	{ "nb"  "N" "sp2" }
>> 	{ "nc"  "N" "sp2" }
>> 	{ "nd"  "N" "sp2" }
>> 	{ "ne"  "N" "sp2" }
>> 	{ "nf"  "N" "sp2" }
>> 	{ "nh"  "N" "sp2" }
>> 	{ "ni"  "N" "sp2" }
>> 	{ "nj"  "N" "sp2" }
>> 	{ "nk"  "N" "sp3" }
>> 	{ "nl"  "N" "sp3" }
>> 	{ "nm"  "N" "sp2" }
>> 	{ "nn"  "N" "sp2" }
>> 	{ "no"  "N" "sp2" }
>> 	{ "np"  "N" "sp3" }
>> 	{ "nq"  "N" "sp3" }
>> 	{ "ns"  "N" "sp2" }
>> 	{ "nt"  "N" "sp2" }
>> 	{ "nu"  "N" "sp2" }
>> 	{ "nv"  "N" "sp2" }
>> 	{ "nx"  "N" "sp3" }
>> 	{ "ny"  "N" "sp3" }
>> 	{ "nz"  "N" "sp3" }
>> 	{ "n+"  "N" "sp3" }
>> 	{ "s"   "S" "sp2" }
>> 	{ "s2"   "S" "sp2" }
>> 	{ "s3"   "S" "sp3" }
>> 	{ "s4"   "S" "sp3" }
>> 	{ "s6"   "S" "sp3" }
>> 	{ "sh"   "S" "sp3" }
>> 	{ "sp"   "S" "sp3" }
>> 	{ "sq"   "S" "sp3" }
>> 	{ "ss"   "S" "sp3" }
>> 	{ "sx"   "S" "sp3" }
>> 	{ "sy"   "S" "sp3" }
>> 	{ "p2"   "P" "sp2" }
>> 	{ "p3"   "P" "sp3" }
>> 	{ "p4"   "P" "sp3" }
>> 	{ "p5"   "P" "sp3" }
>> 	{ "pb"   "P" "sp3" }
>> 	{ "pc"   "P" "sp3" }
>> 	{ "pd"   "P" "sp3" }
>> 	{ "pe"   "P" "sp3" }
>> 	{ "pf"   "P" "sp3" }
>> 	{ "px"   "P" "sp3" }
>> 	{ "py"   "P" "sp3" }
>> 	{ "f"   "F" "sp3" }
>> 	{ "cl"  "Cl" "sp3" }
>> 	{ "br"  "Br" "sp3" }
>> 	{ "i"   "I"  "sp3" }
>> }
>> #
>> #	Load the general force field parameter set.
>> #
>> gaff = loadamberparams gaff2.dat
Loading parameters: /home/student/Structural_bioinformatics/amber20/dat/leap/parm/gaff2.dat
Reading title:
AMBER General Force Field for organic molecules (Version 2.11, May 2016)
> 
> loadamberparams dar.frcmod
Loading parameters: ./dar.frcmod
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
> DAR = loadmol2 dar.mol2
Loading Mol2 file: ./dar.mol2
Reading MOLECULE named DAR
> check DAR
Checking 'DAR'....
Checking parameters for unit 'DAR'.
Checking for bond parameters.
Checking for angle parameters.
Unit is OK.
> saveoff DAR dar.lib
 Creating dar.lib
Saving DAR.
Building topology.
Building atom parameters.
> quit
	Quit

Exiting LEaP: Errors = 0; Warnings = 0; Notes = 0.