AMBER Archive (2006)

Subject: AMBER: Leap adds hydrogens but cannot resolve their type.

From: Paul R Brenner (pbrenne1_at_nd.edu)
Date: Thu Aug 10 2006 - 14:23:55 CDT

Hello,

I googled the list archive but could not find this odd topic covered. I'm
trying to create Amber input files using xleap (all AMBER 9.0) for a small
protein domain (33 residues). I have built NAMD inputs for this domain without
any issues but when I try to create AMBER inputs xleap adds hydrogens and then
reports that it cannot resolve the type. Am I missing a standard library? It
seems that the normal ff03 libs are loaded. I would expect a challenge with
non-standard residues/atoms, but this hydrogen issue has me stumped. Ideas?

Thanks,
Paul

********************

Welcome to LEaP!
Sourcing:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/cmd/leaprc.ff03
Log file: ./leap.log
Loading parameters:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP incl.02/04/99
Loading parameters:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/parm/frcmod.ff03
Reading force field modification type file (frcmod)
Reading title:
Duan et al ff03 phi psi torsions
Loading library:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/lib/ions94.lib
Loading library:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/lib/solvents.lib
Loading library:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/lib/all_nucleic94.lib
Loading library:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/lib/all_aminoct94.lib
Loading library:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/lib/all_aminont94.lib
Loading library:
/afs/nd.edu/i386_linux24/opt/und/amber/x86/amber9/dat/leap/lib/all_amino03.lib
> wwd=loadpdb "1I6C_33res_Mod1.pdb"
Loading PDB file: ./1I6C_33res_Mod1.pdb
Created a new atom named: H within residue: .R<NLYS 1>
Created a new atom named: HB1 within residue: .R<NLYS 1>
Created a new atom named: HG1 within residue: .R<NLYS 1>
Created a new atom named: HD1 within residue: .R<NLYS 1>
Created a new atom named: HE1 within residue: .R<NLYS 1>
Created a new atom named: HB1 within residue: .R<LEU 2>
Created a new atom named: HB1 within residue: .R<PRO 3>
Created a new atom named: HG1 within residue: .R<PRO 3>
Created a new atom named: HD1 within residue: .R<PRO 3>
Created a new atom named: HB1 within residue: .R<PRO 4>
Created a new atom named: HG1 within residue: .R<PRO 4>
Created a new atom named: HD1 within residue: .R<PRO 4>
Created a new atom named: HA1 within residue: .R<GLY 5>
Created a new atom named: HB1 within residue: .R<TRP 6>
Created a new atom named: HB1 within residue: .R<GLU 7>
Created a new atom named: HG1 within residue: .R<GLU 7>
Created a new atom named: HB1 within residue: .R<LYS 8>
Created a new atom named: HG1 within residue: .R<LYS 8>
Created a new atom named: HD1 within residue: .R<LYS 8>
Created a new atom named: HE1 within residue: .R<LYS 8>
Created a new atom named: HB1 within residue: .R<ARG 9>
Created a new atom named: HG1 within residue: .R<ARG 9>
Created a new atom named: HD1 within residue: .R<ARG 9>
Created a new atom named: HB1 within residue: .R<MET 10>
Created a new atom named: HG1 within residue: .R<MET 10>
Created a new atom named: HB1 within residue: .R<SER 11>
Created a new atom named: HB1 within residue: .R<ARG 12>
Created a new atom named: HG1 within residue: .R<ARG 12>
Created a new atom named: HD1 within residue: .R<ARG 12>
Created a new atom named: HB1 within residue: .R<SER 13>
Created a new atom named: HB1 within residue: .R<SER 14>
Created a new atom named: HA1 within residue: .R<GLY 15>
Created a new atom named: HB1 within residue: .R<ARG 16>
Created a new atom named: HG1 within residue: .R<ARG 16>
Created a new atom named: HD1 within residue: .R<ARG 16>
Created a new atom named: HB1 within residue: .R<TYR 18>
Created a new atom named: HB1 within residue: .R<TYR 19>
Created a new atom named: HB1 within residue: .R<PHE 20>
Created a new atom named: HB1 within residue: .R<ASN 21>
Created a new atom named: HB1 within residue: .R<HIE 22>
Created a new atom named: HD1 within residue: .R<HIE 22>
Created a new atom named: HG11 within residue: .R<ILE 23>
Created a new atom named: HB1 within residue: .R<ASN 25>
Created a new atom named: HB1 within residue: .R<SER 27>
Created a new atom named: HB1 within residue: .R<GLN 28>
Created a new atom named: HG1 within residue: .R<GLN 28>
Created a new atom named: HB1 within residue: .R<TRP 29>
Created a new atom named: HB1 within residue: .R<GLU 30>
Created a new atom named: HG1 within residue: .R<GLU 30>
Created a new atom named: HB1 within residue: .R<ARG 31>
Created a new atom named: HG1 within residue: .R<ARG 31>
Created a new atom named: HD1 within residue: .R<ARG 31>
Created a new atom named: HB1 within residue: .R<PRO 32>
Created a new atom named: HG1 within residue: .R<PRO 32>
Created a new atom named: HD1 within residue: .R<PRO 32>
Created a new atom named: HB1 within residue: .R<CSER 33>
  Added missing heavy atom: .R<CSER 33>.A<OXT 12>
  total atoms in file: 550
  Leap added 59 missing atoms according to residue templates:
       1 Heavy
       58 H / lone pairs
  The file contained 56 atoms not in residue templates
> saveAmberParm wwd prmtop prmcrd
Checking Unit.
WARNING: The unperturbed charge of the unit: 4.000000 is not zero.
FATAL: Atom .R<NLYS 1>.A<H 25> does not have a type.
FATAL: Atom .R<NLYS 1>.A<HB1 26> does not have a type.
FATAL: Atom .R<NLYS 1>.A<HG1 27> does not have a type.
FATAL: Atom .R<NLYS 1>.A<HD1 28> does not have a type.
FATAL: Atom .R<NLYS 1>.A<HE1 29> does not have a type.
FATAL: Atom .R<LEU 2>.A<HB1 20> does not have a type.
FATAL: Atom .R<PRO 3>.A<HB1 15> does not have a type.
FATAL: Atom .R<PRO 3>.A<HG1 16> does not have a type.
FATAL: Atom .R<PRO 3>.A<HD1 17> does not have a type.
FATAL: Atom .R<PRO 4>.A<HB1 15> does not have a type.
FATAL: Atom .R<PRO 4>.A<HG1 16> does not have a type.
FATAL: Atom .R<PRO 4>.A<HD1 17> does not have a type.
FATAL: Atom .R<GLY 5>.A<HA1 8> does not have a type.
FATAL: Atom .R<TRP 6>.A<HB1 25> does not have a type.
FATAL: Atom .R<GLU 7>.A<HB1 16> does not have a type.
FATAL: Atom .R<GLU 7>.A<HG1 17> does not have a type.
FATAL: Atom .R<GLU 7>.A<HB1 16> does not have a type.
FATAL: Atom .R<GLU 7>.A<HG1 17> does not have a type.
FATAL: Atom .R<LYS 8>.A<HB1 23> does not have a type.
FATAL: Atom .R<LYS 8>.A<HG1 24> does not have a type.
FATAL: Atom .R<LYS 8>.A<HD1 25> does not have a type.
FATAL: Atom .R<LYS 8>.A<HE1 26> does not have a type.
FATAL: Atom .R<ARG 9>.A<HB1 25> does not have a type.
FATAL: Atom .R<ARG 9>.A<HG1 26> does not have a type.
FATAL: Atom .R<ARG 9>.A<HD1 27> does not have a type.
FATAL: Atom .R<MET 10>.A<HB1 18> does not have a type.
FATAL: Atom .R<MET 10>.A<HG1 19> does not have a type.
FATAL: Atom .R<SER 11>.A<HB1 12> does not have a type.
FATAL: Atom .R<ARG 12>.A<HB1 25> does not have a type.
FATAL: Atom .R<ARG 12>.A<HG1 26> does not have a type.
FATAL: Atom .R<ARG 12>.A<HD1 27> does not have a type.
FATAL: Atom .R<SER 13>.A<HB1 12> does not have a type.
FATAL: Atom .R<SER 14>.A<HB1 12> does not have a type.
FATAL: Atom .R<GLY 15>.A<HA1 8> does not have a type.
FATAL: Atom .R<ARG 16>.A<HB1 25> does not have a type.
FATAL: Atom .R<ARG 16>.A<HG1 26> does not have a type.
FATAL: Atom .R<ARG 16>.A<HD1 27> does not have a type.
FATAL: Atom .R<TYR 18>.A<HB1 22> does not have a type.
FATAL: Atom .R<TYR 19>.A<HB1 22> does not have a type.
FATAL: Atom .R<PHE 20>.A<HB1 21> does not have a type.
FATAL: Atom .R<ASN 21>.A<HB1 15> does not have a type.
FATAL: Atom .R<HIE 22>.A<HB1 18> does not have a type.
FATAL: Atom .R<HIE 22>.A<HD1 19> does not have a type.
FATAL: Atom .R<ILE 23>.A<HG11 20> does not have a type.
FATAL: Atom .R<ASN 25>.A<HB1 15> does not have a type.
FATAL: Atom .R<SER 27>.A<HB1 12> does not have a type.
FATAL: Atom .R<GLN 28>.A<HB1 18> does not have a type.
FATAL: Atom .R<GLN 28>.A<HG1 19> does not have a type.
FATAL: Atom .R<TRP 29>.A<HB1 25> does not have a type.
FATAL: Atom .R<GLU 30>.A<HB1 16> does not have a type.
FATAL: Atom .R<GLU 30>.A<HG1 17> does not have a type.
FATAL: Atom .R<ARG 31>.A<HB1 25> does not have a type.
FATAL: Atom .R<ARG 31>.A<HG1 26> does not have a type.
FATAL: Atom .R<ARG 31>.A<HD1 27> does not have a type.
FATAL: Atom .R<PRO 32>.A<HB1 15> does not have a type.
FATAL: Atom .R<PRO 32>.A<HG1 16> does not have a type.
FATAL: Atom .R<PRO 32>.A<HD1 17> does not have a type.
FATAL: Atom .R<CSER 33>.A<HB1 13> does not have a type.
Failed to generate parameters

*************************
Thanks,
Paul

Paul R Brenner, P.E.
Computer Science and Engineering
The University of Notre Dame

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