log

pdb4amber -i ../../models/w2c_24A_xtal.pdb -o out/w2c_24A_xtal__00_raw_00_clean.pdb  --dry --strip @/H --logfile stdout

==================================================
Summary of pdb4amber for: ../../models/w2c_24A_xtal.pdb
===================================================

----------Chains
The following (original) chains have been found:
A
B
c

---------- Alternate Locations (Original Residues!))

The following residues had alternate locations:
None
-----------Non-standard-resnames


---------- Mising heavy atom(s)

GLU_57 misses 4 heavy atom(s)
ARG_61 misses 4 heavy atom(s)
GLU_114 misses 4 heavy atom(s)
ASP_122 misses 3 heavy atom(s)
ARG_177 misses 6 heavy atom(s)
ARG_204 misses 6 heavy atom(s)
GLU_215 misses 4 heavy atom(s)
LYS_219 misses 4 heavy atom(s)
ASN_221 misses 3 heavy atom(s)
GLU_223 misses 4 heavy atom(s)
ARG_226 misses 6 heavy atom(s)
ARG_247 misses 6 heavy atom(s)
ARG_248 misses 6 heavy atom(s)
ASP_250 misses 3 heavy atom(s)
GLU_252 misses 4 heavy atom(s)
ARG_254 misses 6 heavy atom(s)
ARG_255 misses 6 heavy atom(s)
GLU_266 misses 4 heavy atom(s)
GLU_326 misses 4 heavy atom(s)
ARG_330 misses 4 heavy atom(s)
GLU_383 misses 4 heavy atom(s)
ASP_391 misses 3 heavy atom(s)
ARG_446 misses 6 heavy atom(s)
ARG_473 misses 6 heavy atom(s)
GLU_484 misses 4 heavy atom(s)
LYS_488 misses 4 heavy atom(s)
ASN_490 misses 3 heavy atom(s)
GLU_492 misses 4 heavy atom(s)
ARG_495 misses 6 heavy atom(s)
ARG_516 misses 6 heavy atom(s)
ARG_517 misses 6 heavy atom(s)
ASP_519 misses 3 heavy atom(s)
GLU_521 misses 4 heavy atom(s)
ARG_523 misses 6 heavy atom(s)
ARG_524 misses 6 heavy atom(s)
GLU_535 misses 4 heavy atom(s)
GLU_595 misses 4 heavy atom(s)
ARG_599 misses 4 heavy atom(s)
GLU_652 misses 4 heavy atom(s)
ASP_660 misses 3 heavy atom(s)
ARG_715 misses 6 heavy atom(s)
ARG_742 misses 6 heavy atom(s)
GLU_753 misses 4 heavy atom(s)
LYS_757 misses 4 heavy atom(s)
ASN_759 misses 3 heavy atom(s)
GLU_761 misses 4 heavy atom(s)
ARG_764 misses 6 heavy atom(s)
ARG_785 misses 6 heavy atom(s)
ARG_786 misses 6 heavy atom(s)
ASP_788 misses 3 heavy atom(s)
GLU_790 misses 4 heavy atom(s)
ARG_792 misses 6 heavy atom(s)
ARG_793 misses 6 heavy atom(s)
GLU_804 misses 4 heavy atom(s)
tleap -f out/w2c_24A_xtal__00_raw_00_leap.in
-I: Adding /home/ajasja/.conda/envs/pyro_scripts/dat/leap/prep to search path.
-I: Adding /home/ajasja/.conda/envs/pyro_scripts/dat/leap/lib to search path.
-I: Adding /home/ajasja/.conda/envs/pyro_scripts/dat/leap/parm to search path.
-I: Adding /home/ajasja/.conda/envs/pyro_scripts/dat/leap/cmd to search path.
-f: Source out/w2c_24A_xtal__00_raw_00_leap.in.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./out/w2c_24A_xtal__00_raw_00_leap.in
----- Source: /home/ajasja/.conda/envs/pyro_scripts/dat/leap/cmd/leaprc.protein.ff14SBonlysc
----- Source of /home/ajasja/.conda/envs/pyro_scripts/dat/leap/cmd/leaprc.protein.ff14SBonlysc done
Log file: ./leap.log
Loading parameters: /home/ajasja/.conda/envs/pyro_scripts/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /home/ajasja/.conda/envs/pyro_scripts/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading parameters: /home/ajasja/.conda/envs/pyro_scripts/dat/leap/parm/frcmod.ff99SB14
Reading force field modification type file (frcmod)
Reading title:
ff99SB backbone parameters (Hornak & Simmerling) with ff14SB atom types
Loading library: /home/ajasja/.conda/envs/pyro_scripts/dat/leap/lib/amino12.lib
Loading library: /home/ajasja/.conda/envs/pyro_scripts/dat/leap/lib/aminoct12.lib
Loading library: /home/ajasja/.conda/envs/pyro_scripts/dat/leap/lib/aminont12.lib
Using ArgH and AspGluO modified Bondi2 radii
Loading PDB file: ./out/w2c_24A_xtal__00_raw_00_clean.pdb
  Added missing heavy atom: .R<GLU 57>.A<CG 8>
  Added missing heavy atom: .R<GLU 57>.A<CD 11>
  Added missing heavy atom: .R<GLU 57>.A<OE1 12>
  Added missing heavy atom: .R<GLU 57>.A<OE2 13>
  Added missing heavy atom: .R<ARG 61>.A<NE 14>
  Added missing heavy atom: .R<ARG 61>.A<CZ 16>
  Added missing heavy atom: .R<ARG 61>.A<NH1 17>
  Added missing heavy atom: .R<ARG 61>.A<NH2 20>
  Added missing heavy atom: .R<GLU 114>.A<CG 8>
  Added missing heavy atom: .R<GLU 114>.A<CD 11>
  Added missing heavy atom: .R<GLU 114>.A<OE1 12>
  Added missing heavy atom: .R<GLU 114>.A<OE2 13>
  Added missing heavy atom: .R<ASP 122>.A<CG 8>
  Added missing heavy atom: .R<ASP 122>.A<OD1 9>
  Added missing heavy atom: .R<ASP 122>.A<OD2 10>
  Added missing heavy atom: .R<ARG 177>.A<CG 8>
  Added missing heavy atom: .R<ARG 177>.A<CD 11>
  Added missing heavy atom: .R<ARG 177>.A<NE 14>
  Added missing heavy atom: .R<ARG 177>.A<CZ 16>
  Added missing heavy atom: .R<ARG 177>.A<NH1 17>
  Added missing heavy atom: .R<ARG 177>.A<NH2 20>
  Added missing heavy atom: .R<ARG 204>.A<CG 8>
  Added missing heavy atom: .R<ARG 204>.A<CD 11>
  Added missing heavy atom: .R<ARG 204>.A<NE 14>
  Added missing heavy atom: .R<ARG 204>.A<CZ 16>
  Added missing heavy atom: .R<ARG 204>.A<NH1 17>
  Added missing heavy atom: .R<ARG 204>.A<NH2 20>
  Added missing heavy atom: .R<GLU 215>.A<CG 8>
  Added missing heavy atom: .R<GLU 215>.A<CD 11>
  Added missing heavy atom: .R<GLU 215>.A<OE1 12>
  Added missing heavy atom: .R<GLU 215>.A<OE2 13>
  Added missing heavy atom: .R<LYS 219>.A<CG 8>
  Added missing heavy atom: .R<LYS 219>.A<CD 11>
  Added missing heavy atom: .R<LYS 219>.A<CE 14>
  Added missing heavy atom: .R<LYS 219>.A<NZ 17>
  Added missing heavy atom: .R<ASN 221>.A<CG 8>
  Added missing heavy atom: .R<ASN 221>.A<OD1 9>
  Added missing heavy atom: .R<ASN 221>.A<ND2 10>
  Added missing heavy atom: .R<GLU 223>.A<CG 8>
  Added missing heavy atom: .R<GLU 223>.A<CD 11>
  Added missing heavy atom: .R<GLU 223>.A<OE1 12>
  Added missing heavy atom: .R<GLU 223>.A<OE2 13>
  Added missing heavy atom: .R<ARG 226>.A<CG 8>
  Added missing heavy atom: .R<ARG 226>.A<CD 11>
  Added missing heavy atom: .R<ARG 226>.A<NE 14>
  Added missing heavy atom: .R<ARG 226>.A<CZ 16>
  Added missing heavy atom: .R<ARG 226>.A<NH1 17>
  Added missing heavy atom: .R<ARG 226>.A<NH2 20>
  Added missing heavy atom: .R<ARG 247>.A<CG 8>
  Added missing heavy atom: .R<ARG 247>.A<CD 11>
  Added missing heavy atom: .R<ARG 247>.A<NE 14>
  Added missing heavy atom: .R<ARG 247>.A<CZ 16>
  Added missing heavy atom: .R<ARG 247>.A<NH1 17>
  Added missing heavy atom: .R<ARG 247>.A<NH2 20>
  Added missing heavy atom: .R<ARG 248>.A<CG 8>
  Added missing heavy atom: .R<ARG 248>.A<CD 11>
  Added missing heavy atom: .R<ARG 248>.A<NE 14>
  Added missing heavy atom: .R<ARG 248>.A<CZ 16>
  Added missing heavy atom: .R<ARG 248>.A<NH1 17>
  Added missing heavy atom: .R<ARG 248>.A<NH2 20>
  Added missing heavy atom: .R<ASP 250>.A<CG 8>
  Added missing heavy atom: .R<ASP 250>.A<OD1 9>
  Added missing heavy atom: .R<ASP 250>.A<OD2 10>
  Added missing heavy atom: .R<GLU 252>.A<CG 8>
  Added missing heavy atom: .R<GLU 252>.A<CD 11>
  Added missing heavy atom: .R<GLU 252>.A<OE1 12>
  Added missing heavy atom: .R<GLU 252>.A<OE2 13>
  Added missing heavy atom: .R<ARG 254>.A<CG 8>
  Added missing heavy atom: .R<ARG 254>.A<CD 11>
  Added missing heavy atom: .R<ARG 254>.A<NE 14>
  Added missing heavy atom: .R<ARG 254>.A<CZ 16>
  Added missing heavy atom: .R<ARG 254>.A<NH1 17>
  Added missing heavy atom: .R<ARG 254>.A<NH2 20>
  Added missing heavy atom: .R<ARG 255>.A<CG 8>
  Added missing heavy atom: .R<ARG 255>.A<CD 11>
  Added missing heavy atom: .R<ARG 255>.A<NE 14>
  Added missing heavy atom: .R<ARG 255>.A<CZ 16>
  Added missing heavy atom: .R<ARG 255>.A<NH1 17>
  Added missing heavy atom: .R<ARG 255>.A<NH2 20>
  Added missing heavy atom: .R<GLU 266>.A<CG 8>
  Added missing heavy atom: .R<GLU 266>.A<CD 11>
  Added missing heavy atom: .R<GLU 266>.A<OE1 12>
  Added missing heavy atom: .R<GLU 266>.A<OE2 13>
  Added missing heavy atom: .R<CARG 269>.A<OXT 25>
  Added missing heavy atom: .R<GLU 326>.A<CG 8>
  Added missing heavy atom: .R<GLU 326>.A<CD 11>
  Added missing heavy atom: .R<GLU 326>.A<OE1 12>
  Added missing heavy atom: .R<GLU 326>.A<OE2 13>
  Added missing heavy atom: .R<ARG 330>.A<NE 14>
  Added missing heavy atom: .R<ARG 330>.A<CZ 16>
  Added missing heavy atom: .R<ARG 330>.A<NH1 17>
  Added missing heavy atom: .R<ARG 330>.A<NH2 20>
  Added missing heavy atom: .R<GLU 383>.A<CG 8>
  Added missing heavy atom: .R<GLU 383>.A<CD 11>
  Added missing heavy atom: .R<GLU 383>.A<OE1 12>
  Added missing heavy atom: .R<GLU 383>.A<OE2 13>
  Added missing heavy atom: .R<ASP 391>.A<CG 8>
  Added missing heavy atom: .R<ASP 391>.A<OD1 9>
  Added missing heavy atom: .R<ASP 391>.A<OD2 10>
  Added missing heavy atom: .R<ARG 446>.A<CG 8>
  Added missing heavy atom: .R<ARG 446>.A<CD 11>
  Added missing heavy atom: .R<ARG 446>.A<NE 14>
  Added missing heavy atom: .R<ARG 446>.A<CZ 16>
  Added missing heavy atom: .R<ARG 446>.A<NH1 17>
  Added missing heavy atom: .R<ARG 446>.A<NH2 20>
  Added missing heavy atom: .R<ARG 473>.A<CG 8>
  Added missing heavy atom: .R<ARG 473>.A<CD 11>
  Added missing heavy atom: .R<ARG 473>.A<NE 14>
  Added missing heavy atom: .R<ARG 473>.A<CZ 16>
  Added missing heavy atom: .R<ARG 473>.A<NH1 17>
  Added missing heavy atom: .R<ARG 473>.A<NH2 20>
  Added missing heavy atom: .R<GLU 484>.A<CG 8>
  Added missing heavy atom: .R<GLU 484>.A<CD 11>
  Added missing heavy atom: .R<GLU 484>.A<OE1 12>
  Added missing heavy atom: .R<GLU 484>.A<OE2 13>
  Added missing heavy atom: .R<LYS 488>.A<CG 8>
  Added missing heavy atom: .R<LYS 488>.A<CD 11>
  Added missing heavy atom: .R<LYS 488>.A<CE 14>
  Added missing heavy atom: .R<LYS 488>.A<NZ 17>
  Added missing heavy atom: .R<ASN 490>.A<CG 8>
  Added missing heavy atom: .R<ASN 490>.A<OD1 9>
  Added missing heavy atom: .R<ASN 490>.A<ND2 10>
  Added missing heavy atom: .R<GLU 492>.A<CG 8>
  Added missing heavy atom: .R<GLU 492>.A<CD 11>
  Added missing heavy atom: .R<GLU 492>.A<OE1 12>
  Added missing heavy atom: .R<GLU 492>.A<OE2 13>
  Added missing heavy atom: .R<ARG 495>.A<CG 8>
  Added missing heavy atom: .R<ARG 495>.A<CD 11>
  Added missing heavy atom: .R<ARG 495>.A<NE 14>
  Added missing heavy atom: .R<ARG 495>.A<CZ 16>
  Added missing heavy atom: .R<ARG 495>.A<NH1 17>
  Added missing heavy atom: .R<ARG 495>.A<NH2 20>
  Added missing heavy atom: .R<ARG 516>.A<CG 8>
  Added missing heavy atom: .R<ARG 516>.A<CD 11>
  Added missing heavy atom: .R<ARG 516>.A<NE 14>
  Added missing heavy atom: .R<ARG 516>.A<CZ 16>
  Added missing heavy atom: .R<ARG 516>.A<NH1 17>
  Added missing heavy atom: .R<ARG 516>.A<NH2 20>
  Added missing heavy atom: .R<ARG 517>.A<CG 8>
  Added missing heavy atom: .R<ARG 517>.A<CD 11>
  Added missing heavy atom: .R<ARG 517>.A<NE 14>
  Added missing heavy atom: .R<ARG 517>.A<CZ 16>
  Added missing heavy atom: .R<ARG 517>.A<NH1 17>
  Added missing heavy atom: .R<ARG 517>.A<NH2 20>
  Added missing heavy atom: .R<ASP 519>.A<CG 8>
  Added missing heavy atom: .R<ASP 519>.A<OD1 9>
  Added missing heavy atom: .R<ASP 519>.A<OD2 10>
  Added missing heavy atom: .R<GLU 521>.A<CG 8>
  Added missing heavy atom: .R<GLU 521>.A<CD 11>
  Added missing heavy atom: .R<GLU 521>.A<OE1 12>
  Added missing heavy atom: .R<GLU 521>.A<OE2 13>
  Added missing heavy atom: .R<ARG 523>.A<CG 8>
  Added missing heavy atom: .R<ARG 523>.A<CD 11>
  Added missing heavy atom: .R<ARG 523>.A<NE 14>
  Added missing heavy atom: .R<ARG 523>.A<CZ 16>
  Added missing heavy atom: .R<ARG 523>.A<NH1 17>
  Added missing heavy atom: .R<ARG 523>.A<NH2 20>
  Added missing heavy atom: .R<ARG 524>.A<CG 8>
  Added missing heavy atom: .R<ARG 524>.A<CD 11>
  Added missing heavy atom: .R<ARG 524>.A<NE 14>
  Added missing heavy atom: .R<ARG 524>.A<CZ 16>
  Added missing heavy atom: .R<ARG 524>.A<NH1 17>
  Added missing heavy atom: .R<ARG 524>.A<NH2 20>
  Added missing heavy atom: .R<GLU 535>.A<CG 8>
  Added missing heavy atom: .R<GLU 535>.A<CD 11>
  Added missing heavy atom: .R<GLU 535>.A<OE1 12>
  Added missing heavy atom: .R<GLU 535>.A<OE2 13>
  Added missing heavy atom: .R<CARG 538>.A<OXT 25>
  Added missing heavy atom: .R<GLU 595>.A<CG 8>
  Added missing heavy atom: .R<GLU 595>.A<CD 11>
  Added missing heavy atom: .R<GLU 595>.A<OE1 12>
  Added missing heavy atom: .R<GLU 595>.A<OE2 13>
  Added missing heavy atom: .R<ARG 599>.A<NE 14>
  Added missing heavy atom: .R<ARG 599>.A<CZ 16>
  Added missing heavy atom: .R<ARG 599>.A<NH1 17>
  Added missing heavy atom: .R<ARG 599>.A<NH2 20>
  Added missing heavy atom: .R<GLU 652>.A<CG 8>
  Added missing heavy atom: .R<GLU 652>.A<CD 11>
  Added missing heavy atom: .R<GLU 652>.A<OE1 12>
  Added missing heavy atom: .R<GLU 652>.A<OE2 13>
  Added missing heavy atom: .R<ASP 660>.A<CG 8>
  Added missing heavy atom: .R<ASP 660>.A<OD1 9>
  Added missing heavy atom: .R<ASP 660>.A<OD2 10>
  Added missing heavy atom: .R<ARG 715>.A<CG 8>
  Added missing heavy atom: .R<ARG 715>.A<CD 11>
  Added missing heavy atom: .R<ARG 715>.A<NE 14>
  Added missing heavy atom: .R<ARG 715>.A<CZ 16>
  Added missing heavy atom: .R<ARG 715>.A<NH1 17>
  Added missing heavy atom: .R<ARG 715>.A<NH2 20>
  Added missing heavy atom: .R<ARG 742>.A<CG 8>
  Added missing heavy atom: .R<ARG 742>.A<CD 11>
  Added missing heavy atom: .R<ARG 742>.A<NE 14>
  Added missing heavy atom: .R<ARG 742>.A<CZ 16>
  Added missing heavy atom: .R<ARG 742>.A<NH1 17>
  Added missing heavy atom: .R<ARG 742>.A<NH2 20>
  Added missing heavy atom: .R<GLU 753>.A<CG 8>
  Added missing heavy atom: .R<GLU 753>.A<CD 11>
  Added missing heavy atom: .R<GLU 753>.A<OE1 12>
  Added missing heavy atom: .R<GLU 753>.A<OE2 13>
  Added missing heavy atom: .R<LYS 757>.A<CG 8>
  Added missing heavy atom: .R<LYS 757>.A<CD 11>
  Added missing heavy atom: .R<LYS 757>.A<CE 14>
  Added missing heavy atom: .R<LYS 757>.A<NZ 17>
  Added missing heavy atom: .R<ASN 759>.A<CG 8>
  Added missing heavy atom: .R<ASN 759>.A<OD1 9>
  Added missing heavy atom: .R<ASN 759>.A<ND2 10>
  Added missing heavy atom: .R<GLU 761>.A<CG 8>
  Added missing heavy atom: .R<GLU 761>.A<CD 11>
  Added missing heavy atom: .R<GLU 761>.A<OE1 12>
  Added missing heavy atom: .R<GLU 761>.A<OE2 13>
  Added missing heavy atom: .R<ARG 764>.A<CG 8>
  Added missing heavy atom: .R<ARG 764>.A<CD 11>
  Added missing heavy atom: .R<ARG 764>.A<NE 14>
  Added missing heavy atom: .R<ARG 764>.A<CZ 16>
  Added missing heavy atom: .R<ARG 764>.A<NH1 17>
  Added missing heavy atom: .R<ARG 764>.A<NH2 20>
  Added missing heavy atom: .R<ARG 785>.A<CG 8>
  Added missing heavy atom: .R<ARG 785>.A<CD 11>
  Added missing heavy atom: .R<ARG 785>.A<NE 14>
  Added missing heavy atom: .R<ARG 785>.A<CZ 16>
  Added missing heavy atom: .R<ARG 785>.A<NH1 17>
  Added missing heavy atom: .R<ARG 785>.A<NH2 20>
  Added missing heavy atom: .R<ARG 786>.A<CG 8>
  Added missing heavy atom: .R<ARG 786>.A<CD 11>
  Added missing heavy atom: .R<ARG 786>.A<NE 14>
  Added missing heavy atom: .R<ARG 786>.A<CZ 16>
  Added missing heavy atom: .R<ARG 786>.A<NH1 17>
  Added missing heavy atom: .R<ARG 786>.A<NH2 20>
  Added missing heavy atom: .R<ASP 788>.A<CG 8>
  Added missing heavy atom: .R<ASP 788>.A<OD1 9>
  Added missing heavy atom: .R<ASP 788>.A<OD2 10>
  Added missing heavy atom: .R<GLU 790>.A<CG 8>
  Added missing heavy atom: .R<GLU 790>.A<CD 11>
  Added missing heavy atom: .R<GLU 790>.A<OE1 12>
  Added missing heavy atom: .R<GLU 790>.A<OE2 13>
  Added missing heavy atom: .R<ARG 792>.A<CG 8>
  Added missing heavy atom: .R<ARG 792>.A<CD 11>
  Added missing heavy atom: .R<ARG 792>.A<NE 14>
  Added missing heavy atom: .R<ARG 792>.A<CZ 16>
  Added missing heavy atom: .R<ARG 792>.A<NH1 17>
  Added missing heavy atom: .R<ARG 792>.A<NH2 20>
  Added missing heavy atom: .R<ARG 793>.A<CG 8>
  Added missing heavy atom: .R<ARG 793>.A<CD 11>
  Added missing heavy atom: .R<ARG 793>.A<NE 14>
  Added missing heavy atom: .R<ARG 793>.A<CZ 16>
  Added missing heavy atom: .R<ARG 793>.A<NH1 17>
  Added missing heavy atom: .R<ARG 793>.A<NH2 20>
  Added missing heavy atom: .R<GLU 804>.A<CG 8>
  Added missing heavy atom: .R<GLU 804>.A<CD 11>
  Added missing heavy atom: .R<GLU 804>.A<OE1 12>
  Added missing heavy atom: .R<GLU 804>.A<OE2 13>
  Added missing heavy atom: .R<CARG 807>.A<OXT 25>
  total atoms in file: 6129
  Leap added 6765 missing atoms according to residue templates:
       252 Heavy
       6513 H / lone pairs
Checking Unit.

/home/ajasja/.conda/envs/pyro_scripts/bin/teLeap: Warning!
The unperturbed charge of the unit (-33.000000) is not zero.

/home/ajasja/.conda/envs/pyro_scripts/bin/teLeap: Note.
Ignoring the warning from Unit Checking.

Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
 total 2379 improper torsions applied
Building H-Bond parameters.
Incorporating Non-Bonded adjustments.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
  (Residues lacking connect0/connect1 - 
   these don't have chain types marked:

	res	total affected

	CARG	3
	NGLY	3
  )
 (no restraints)
	Quit

Exiting LEaP: Errors = 0; Warnings = 1; Notes = 1.
Building system...
Done in 1.66 s.