LassoHTP occasionally fails on certain input sequences

[pmccaffrey6]

Hello,

First of all, thank you for this wonderful tool and paper. I've noticed that I experience errors with certain lasso peptides like, for example, fusilassin (whose aa sequence is WYTAEWGLELIFVFPRFI).

I looked at the leap_P2PwL.out, leap.out, and min.out files and I noticed that the error seems to occur in the PDB2PDBwLeap step. The following is from the leap_P2PwL.out file:

-I: Adding /Users/pmccaffrey/Downloads/amber22/dat/leap/lib to search path.
-I: Adding /Users/pmccaffrey/Downloads/amber22/dat/leap/parm to search path.
-I: Adding /Users/pmccaffrey/Downloads/amber22/dat/leap/cmd to search path.
-s: Ignoring all leaprc startup files.
-f: Source ../../../Users/pmccaffrey/LassoHTP/pragma_work/cache/leap_P2PwL.in.

Welcome to LEaP!
Sourcing: ../../../Users/pmccaffrey/LassoHTP/pragma_work/cache/leap_P2PwL.in
----- Source: ./leaprc.protein.ff14SBmod
----- Source of ./leaprc.protein.ff14SBmod done
Log file: ./leap.log
Loading parameters: /Users/pmccaffrey/Downloads/amber22/dat/leap/parm/parm10.dat
Reading title:
PARM99 + frcmod.ff99SB + frcmod.parmbsc0 + OL3 for RNA
Loading parameters: /Users/pmccaffrey/Downloads/amber22/dat/leap/parm/frcmod.ff14SB
Reading force field modification type file (frcmod)
Reading title:
ff14SB protein backbone and sidechain parameters
Loading library: /Users/pmccaffrey/Downloads/amber22/dat/leap/lib/amino12.lib
Loading library: /Users/pmccaffrey/Downloads/amber22/dat/leap/lib/aminoct12.lib
Loading library: /Users/pmccaffrey/Downloads/amber22/dat/leap/lib/aminont12.lib
Loading parameters: ./ligands/ligand_GLX.frcmod1
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading parameters: ./ligands/ligand_GLX.frcmod2
Reading force field modification type file (frcmod)
Reading title:
Remark line goes here
Loading Prep file: ./ligands/ligand_GLX.prepin
Loading PDB file: ../../../Users/pmccaffrey/LassoHTP/pragma_work/cache/8e_11_0_AA1W_AA2Y_AA3T_AA4A_AA5E_AA6W_AA7G_AA9L_AA10I_AA11F_AA12V_AA13F_AA14P_AA15R_AA16F_AA17I_AA18Y_AA19G_tmp.pdb
Created a new atom named: H within residue: .R<NTRP 1>
  Added missing heavy atom: .R<NTRP 1>.A<CG 10>
  Added missing heavy atom: .R<NTRP 1>.A<CD1 11>
  Added missing heavy atom: .R<NTRP 1>.A<CD2 24>
  Added missing heavy atom: .R<NTRP 1>.A<NE1 13>
  Added missing heavy atom: .R<NTRP 1>.A<CE2 15>
  Added missing heavy atom: .R<NTRP 1>.A<CE3 22>
  Added missing heavy atom: .R<NTRP 1>.A<CZ2 16>
  Added missing heavy atom: .R<NTRP 1>.A<CZ3 20>
  Added missing heavy atom: .R<NTRP 1>.A<CH2 18>
  Added missing heavy atom: .R<TYR 2>.A<CG 8>
  Added missing heavy atom: .R<TYR 2>.A<CD1 9>
  Added missing heavy atom: .R<TYR 2>.A<CD2 18>
  Added missing heavy atom: .R<TYR 2>.A<CE1 11>
  Added missing heavy atom: .R<TYR 2>.A<CE2 16>
  Added missing heavy atom: .R<TYR 2>.A<CZ 13>
  Added missing heavy atom: .R<TYR 2>.A<OH 14>
  Added missing heavy atom: .R<THR 3>.A<CG2 7>
  Added missing heavy atom: .R<THR 3>.A<OG1 11>
  Added missing heavy atom: .R<GLU 5>.A<CG 8>
  Added missing heavy atom: .R<GLU 5>.A<CD 11>
  Added missing heavy atom: .R<GLU 5>.A<OE1 12>
  Added missing heavy atom: .R<GLU 5>.A<OE2 13>
  Added missing heavy atom: .R<TRP 6>.A<CG 8>
  Added missing heavy atom: .R<TRP 6>.A<CD1 9>
  Added missing heavy atom: .R<TRP 6>.A<CD2 22>
  Added missing heavy atom: .R<TRP 6>.A<NE1 11>
  Added missing heavy atom: .R<TRP 6>.A<CE2 13>
  Added missing heavy atom: .R<TRP 6>.A<CE3 20>
  Added missing heavy atom: .R<TRP 6>.A<CZ2 14>
  Added missing heavy atom: .R<TRP 6>.A<CZ3 18>
  Added missing heavy atom: .R<TRP 6>.A<CH2 16>
  Added missing heavy atom: .R<LEU 9>.A<CG 8>
  Added missing heavy atom: .R<LEU 9>.A<CD1 10>
  Added missing heavy atom: .R<LEU 9>.A<CD2 14>
  Added missing heavy atom: .R<ILE 10>.A<CG2 7>
  Added missing heavy atom: .R<ILE 10>.A<CG1 11>
  Added missing heavy atom: .R<ILE 10>.A<CD1 14>
  Added missing heavy atom: .R<PHE 11>.A<CG 8>
  Added missing heavy atom: .R<PHE 11>.A<CD1 9>
  Added missing heavy atom: .R<PHE 11>.A<CD2 17>
  Added missing heavy atom: .R<PHE 11>.A<CE1 11>
  Added missing heavy atom: .R<PHE 11>.A<CE2 15>
  Added missing heavy atom: .R<PHE 11>.A<CZ 13>
  Added missing heavy atom: .R<VAL 12>.A<CG1 7>
  Added missing heavy atom: .R<VAL 12>.A<CG2 11>
  Added missing heavy atom: .R<PHE 13>.A<CG 8>
  Added missing heavy atom: .R<PHE 13>.A<CD1 9>
  Added missing heavy atom: .R<PHE 13>.A<CD2 17>
  Added missing heavy atom: .R<PHE 13>.A<CE1 11>
  Added missing heavy atom: .R<PHE 13>.A<CE2 15>
  Added missing heavy atom: .R<PHE 13>.A<CZ 13>
  Added missing heavy atom: .R<PRO 14>.A<CG 5>
  Added missing heavy atom: .R<PRO 14>.A<CD 2>
  Added missing heavy atom: .R<ARG 15>.A<CG 8>
  Added missing heavy atom: .R<ARG 15>.A<CD 11>
  Added missing heavy atom: .R<ARG 15>.A<NE 14>
  Added missing heavy atom: .R<ARG 15>.A<CZ 16>
  Added missing heavy atom: .R<ARG 15>.A<NH1 17>
  Added missing heavy atom: .R<ARG 15>.A<NH2 20>
  Added missing heavy atom: .R<PHE 16>.A<CG 8>
  Added missing heavy atom: .R<PHE 16>.A<CD1 9>
  Added missing heavy atom: .R<PHE 16>.A<CD2 17>
  Added missing heavy atom: .R<PHE 16>.A<CE1 11>
  Added missing heavy atom: .R<PHE 16>.A<CE2 15>
  Added missing heavy atom: .R<PHE 16>.A<CZ 13>
  Added missing heavy atom: .R<ILE 17>.A<CG2 7>
  Added missing heavy atom: .R<ILE 17>.A<CG1 11>
  Added missing heavy atom: .R<ILE 17>.A<CD1 14>
  Added missing heavy atom: .R<TYR 18>.A<CG 8>
  Added missing heavy atom: .R<TYR 18>.A<CD1 9>
  Added missing heavy atom: .R<TYR 18>.A<CD2 18>
  Added missing heavy atom: .R<TYR 18>.A<CE1 11>
  Added missing heavy atom: .R<TYR 18>.A<CE2 16>
  Added missing heavy atom: .R<TYR 18>.A<CZ 13>
  Added missing heavy atom: .R<TYR 18>.A<OH 14>
Created a new atom named: OXT within residue: .R<ALA 20>
Created a new atom named: HXT within residue: .R<ALA 20>
  Added missing heavy atom: .R<ALA 20>.A<N 1>
  Added missing heavy atom: .R<ALA 21>.A<N 1>
  Added missing heavy atom: .R<ALA 21>.A<CA 3>
  Added missing heavy atom: .R<ALA 21>.A<CB 5>
  Added missing heavy atom: .R<ALA 21>.A<C 9>
  Added missing heavy atom: .R<ALA 21>.A<O 10>
  Added missing heavy atom: .R<CALA 22>.A<CA 3>
  Added missing heavy atom: .R<CALA 22>.A<CB 5>
  Added missing heavy atom: .R<CALA 22>.A<C 9>
  Added missing heavy atom: .R<CALA 22>.A<O 10>
  Added missing heavy atom: .R<CALA 22>.A<OXT 11>
  total atoms in file: 147
  Leap added 217 missing atoms according to residue templates:
       86 Heavy
       131 H / lone pairs
  The file contained 3 atoms not in residue templates
Writing pdb file: ../../../Users/pmccaffrey/LassoHTP/pragma_work/8e_11_0_AA1W_AA2Y_AA3T_AA4A_AA5E_AA6W_AA7G_AA9L_AA10I_AA11F_AA12V_AA13F_AA14P_AA15R_AA16F_AA17I_AA18Y_AA19G.pdb

/Users/pmccaffrey/Downloads/amber22/bin/teLeap: Warning!
 Converting N-terminal residue name to PDB format: NTRP -> TRP

/Users/pmccaffrey/Downloads/amber22/bin/teLeap: Warning!
 Converting C-terminal residue name to PDB format: CALA -> ALA
Checking Unit.

/Users/pmccaffrey/Downloads/amber22/bin/teLeap: Warning!
There is a bond of 4.936 angstroms between C and N atoms:
-------  .R<ALA 21>.A<C 9> and .R<CALA 22>.A<N 1>

/Users/pmccaffrey/Downloads/amber22/bin/teLeap: Warning!
There is a bond of 3.992 angstroms between N and H atoms:
-------  .R<ALA 21>.A<N 1> and .R<ALA 21>.A<H 2>
FATAL:  Atom .R<NTRP 1>.A<H 27> does not have a type.
FATAL:  Atom .R<ALA 20>.A<OXT 11> does not have a type.
FATAL:  Atom .R<ALA 20>.A<HXT 12> does not have a type.

/Users/pmccaffrey/Downloads/amber22/bin/teLeap: Fatal Error!
Failed to generate parameters

Exiting LEaP: Errors = 1; Warnings = 4; Notes = 0.

Trying this with a few more sequence variations, it seems like this error occurs sometimes and doesn't occur sometimes and I wonder if it's caused by the presence of certain residues. Would you have any idea what really might be causing this and how I might resolve this issue?

Sincerely,
-Peter