Hi,
The atom name issue is usually because the residue or atom names in your
mol2 file don't match what's in your parameter files- they have to be
identical, so that could be what's up.
And I may have missed it in scanning your log, but is there a reason why
you haven't loaded your .lib files? I believe those tend to contain the
atom names for your atoms.
Best,
Kenneth
On Fri, Jul 10, 2015 at 4:36 PM, Evans, Shalton <shalton.ccs.msstate.edu>
wrote:
>
> ________________________________
>
>
>
> Good Day,
>
>
> I am trying to generate a .prmtop file for a non-conventional system. I
> loaded all of parameter files in to Leap and was prompted with errors on
> every single atom. "FATAL: Atom () does not have a type. I saw people
> having trouble with this in the past and tried applying their solutions but
> nothing seems to work. Below is the Leap output when I attempt to create
> the .prmtop file.
>
>
>
>
> $AMBERHOME/bin/tleap -s -f $AMBERHOME/dat/leap/cmd/leaprc.ff99SB
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/prep to search path.
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/lib to search path.
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/parm to search path.
>
> -I: Adding /usr/local/amber10/x86_64/dat/leap/cmd to search path.
>
> -s: Ignoring startup file: leaprc
>
> -f: Source /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.ff99SB.
>
>
> Welcome to LEaP!
>
> Sourcing: /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.ff99SB
>
> Log file: ./leap.log
>
> Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/parm99.dat
>
> Reading title:
>
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
>
> Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/frcmod.ff99SB
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> Modification/update of parm99.dat (Hornak & Simmerling)
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_nucleic94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_amino94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_aminoct94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/all_aminont94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/ions94.lib
>
> Loading library: /usr/local/amber10/x86_64/dat/leap/lib/solvents.lib
>
> > source leaprc.gaff
>
> ----- Source: /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff
>
> ----- Source of /usr/local/amber10/x86_64/dat/leap/cmd/leaprc.gaff done
>
> Log file: ./leap.log
>
> Loading parameters: /usr/local/amber10/x86_64/dat/leap/parm/gaff.dat
>
> Reading title:
>
> AMBER General Force Field for organic mol., add. info. at the end (June,
> 2003)
>
> > dmin_res=loadpdb dmin_res.pdb
>
> Loading PDB file: ./dmin_res.pdb
>
> -- residue 1: duplicate [ C10] atoms (total 11)
>
> -- residue 1: duplicate [ C11] atoms (total 11)
>
> -- residue 1: duplicate [ C12] atoms (total 11)
>
> -- residue 1: duplicate [ C13] atoms (total 11)
>
> -- residue 1: duplicate [ C14] atoms (total 11)
>
> -- residue 1: duplicate [ C15] atoms (total 5)
>
> -- residue 1: duplicate [ CC1] atoms (total 7)
>
> -- residue 2: duplicate [ C10] atoms (total 11)
>
> -- residue 2: duplicate [ C11] atoms (total 11)
>
> -- residue 2: duplicate [ C12] atoms (total 11)
>
> -- residue 2: duplicate [ C13] atoms (total 11)
>
> -- residue 2: duplicate [ C14] atoms (total 11)
>
> -- residue 2: duplicate [ C15] atoms (total 5)
>
> -- residue 2: duplicate [ CC1] atoms (total 7)
>
> -- residue 3: duplicate [ C10] atoms (total 11)
>
> -- residue 3: duplicate [ C11] atoms (total 11)
>
> -- residue 3: duplicate [ C12] atoms (total 11)
>
> -- residue 3: duplicate [ C13] atoms (total 11)
>
> -- residue 3: duplicate [ C14] atoms (total 11)
>
> -- residue 3: duplicate [ C15] atoms (total 5)
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> Warning: Atom names in each residue should be unique.
>
> (Same-name atoms are handled by using the first
>
> occurrence and by ignoring the rest.
>
> Frequently duplicate atom names stem from alternate
>
> conformations in the PDB file.)
>
>
> Unknown residue: GRA number: 0 type: Terminal/beginning
>
> ..relaxing end constraints to try for a dbase match
>
> -no luck
>
> Unknown residue: GRA number: 1 type: Nonterminal
>
> Unknown residue: GRA number: 2 type: Nonterminal
>
> Unknown residue: GRA number: 3 type: Nonterminal
>
> Unknown residue: GRA number: 4 type: Nonterminal
>
> Unknown residue: GRA number: 5 type: Nonterminal
>
> Unknown residue: GRA number: 6 type: Nonterminal
>
> Unknown residue: GRA number: 7 type: Nonterminal
>
> Unknown residue: PCB number: 8 type: Nonterminal
>
> Unknown residue: PCA number: 9 type: Nonterminal
>
> Unknown residue: PCB number: 10 type: Nonterminal
>
> Unknown residue: PCA number: 11 type: Nonterminal
>
> Unknown residue: PCB number: 12 type: Nonterminal
>
> Unknown residue: PCA number: 13 type: Nonterminal
>
> Unknown residue: PCB number: 14 type: Nonterminal
>
> Unknown residue: PCA number: 15 type: Nonterminal
>
> Unknown residue: PCB number: 16 type: Nonterminal
>
> Unknown residue: PCA number: 17 type: Nonterminal
>
> Unknown residue: PCB number: 18 type: Nonterminal
>
> Unknown residue: PCA number: 19 type: Nonterminal
>
> Unknown residue: PCB number: 20 type: Nonterminal
>
> Unknown residue: PCA number: 21 type: Nonterminal
>
> Unknown residue: PCB number: 22 type: Nonterminal
>
> Unknown residue: PCA number: 23 type: Nonterminal
>
> Unknown residue: PCB number: 24 type: Nonterminal
>
> Unknown residue: PCA number: 25 type: Nonterminal
>
> .
> .
> .
> .
> .
> .
>
> Unknown residue: PCA number: 347 type: Nonterminal
>
> Unknown residue: PCB number: 348 type: Nonterminal
>
> Unknown residue: PCA number: 349 type: Nonterminal
>
> Unknown residue: PCB number: 350 type: Nonterminal
>
> Unknown residue: PCA number: 351 type: Nonterminal
>
> Unknown residue: PCB number: 352 type: Nonterminal
>
> Unknown residue: PCA number: 353 type: Nonterminal
>
> Unknown residue: PCB number: 354 type: Nonterminal
>
> Unknown residue: PCA number: 355 type: Terminal/last
>
> ..relaxing end constraints to try for a dbase match
>
> -no luck
>
> Creating new UNIT for residue: GRA sequence: 1
>
> Created a new atom named: C1 within residue: .R<GRA 1>
>
> Created a new atom named: H30 within residue: .R<GRA 1>
>
> Created a new atom named: C2 within residue: .R<GRA 1>
>
> Created a new atom named: H29 within residue: .R<GRA 1>
>
> Created a new atom named: C3 within residue: .R<GRA 1>
>
> Created a new atom named: C4 within residue: .R<GRA 1>
>
> Created a new atom named: C5 within residue: .R<GRA 1>
>
> Created a new atom named: C6 within residue: .R<GRA 1>
>
> Created a new atom named: C49 within residue: .R<GRA 1>
>
> Created a new atom named: C50 within residue: .R<GRA 1>
>
> Created a new atom named: 3HH within residue: .R<GRA 1>
>
> Created a new atom named: C51 within residue: .R<GRA 1>
>
> Created a new atom named: 1H1 within residue: .R<GRA 1>
>
> Created a new atom named: C52 within residue: .R<GRA 1>
>
> Created a new atom named: C53 within residue: .R<GRA 1>
>
> Created a new atom named: C54 within residue: .R<GRA 1>
>
> Created a new atom named: C58 within residue: .R<GRA 1>
>
> Created a new atom named: C10 within residue: .R<GRA 1>
>
> Created a new atom named: C9 within residue: .R<GRA 1>
>
> Created a new atom named: C8 within residue: .R<GRA 1>
>
> Created a new atom named: C7 within residue: .R<GRA 1>
>
> .
>
> .
>
> .
>
> .
>
> .
>
> Created a new atom named: H10 within residue: .R<GRA 1>
>
> Created a new atom named: 2H2 within residue: .R<GRA 1>
>
> Created a new atom named: 3H2 within residue: .R<GRA 1>
>
> Creating new UNIT for residue: GRA sequence: 2
>
> Created a new atom named: C1 within residue: .R<GRA 2>
>
> Created a new atom named: H30 within residue: .R<GRA 2>
>
> Created a new atom named: C2 within residue: .R<GRA 2>
>
> Created a new atom named: H29 within residue: .R<GRA 2>
>
> Created a new atom named: C3 within residue: .R<GRA 2>
>
> Created a new atom named: C4 within residue: .R<GRA 2>
>
> Created a new atom named: C5 within residue: .R<GRA 2>
>
> Created a new atom named: C6 within residue: .R<GRA 2>
>
> Created a new atom named: C49 within residue: .R<GRA 2>
>
> Created a new atom named: C50 within residue: .R<GRA 2>
>
> Created a new atom named: 3HH within residue: .R<GRA 2>
>
> .
> .
> .
> .
> .
>
> Created a new atom named: H9 within residue: .R<GRA 2>
>
> Created a new atom named: H10 within residue: .R<GRA 2>
>
> Created a new atom named: 2H2 within residue: .R<GRA 2>
>
> Created a new atom named: 3H2 within residue: .R<GRA 2>
>
> Creating new UNIT for residue: GRA sequence: 3
>
> Created a new atom named: C1 within residue: .R<GRA 3>
>
> Created a new atom named: H30 within residue: .R<GRA 3>
>
> Created a new atom named: C2 within residue: .R<GRA 3>
>
> Created a new atom named: H29 within residue: .R<GRA 3>
>
> Created a new atom named: C3 within residue: .R<GRA 3>
>
> Created a new atom named: C4 within residue: .R<GRA 3>
>
> Created a new atom named: C5 within residue: .R<GRA 3>
>
> Created a new atom named: C6 within residue: .R<GRA 3>
>
> Created a new atom named: C49 within residue: .R<GRA 3>
>
> Created a new atom named: C50 within residue: .R<GRA 3>
>
> Created a new atom named: 3HH within residue: .R<GRA 3>
>
> .
> .
> .
> .
> .
>
> Created a new atom named: H8 within residue: .R<GRA 3>
>
> Created a new atom named: H9 within residue: .R<GRA 3>
>
> Created a new atom named: H10 within residue: .R<GRA 3>
>
> Created a new atom named: 2H2 within residue: .R<GRA 3>
>
> Created a new atom named: 3H2 within residue: .R<GRA 3>
>
> Creating new UNIT for residue: GRA sequence: 4
>
> Created a new atom named: C1 within residue: .R<GRA 4>
>
> Created a new atom named: H30 within residue: .R<GRA 4>
>
> Created a new atom named: C2 within residue: .R<GRA 4>
>
> Created a new atom named: H29 within residue: .R<GRA 4>
>
> Created a new atom named: C3 within residue: .R<GRA 4>
>
> Created a new atom named: C4 within residue: .R<GRA 4>
>
> Created a new atom named: C5 within residue: .R<GRA 4>
>
> Created a new atom named: C6 within residue: .R<GRA 4>
>
> Created a new atom named: C49 within residue: .R<GRA 4>
>
> Created a new atom named: C50 within residue: .R<GRA 4>
>
> Created a new atom named: 3HH within residue: .R<GRA 4>
>
>
> .
>
> .
>
> .
>
> .
>
> .
>
> .
>
> Created a new atom named: C76 within residue: .R<GRA 4>
>
> Created a new atom named: C79 within residue: .R<GRA 4>
>
> Created a new atom named: H36 within residue: .R<GRA 4>
>
> Created a new atom named: 1HH within residue: .R<GRA 4>
>
> Created a new atom named: H8 within residue: .R<GRA 4>
>
> Created a new atom named: H9 within residue: .R<GRA 4>
>
> Created a new atom named: H10 within residue: .R<GRA 4>
>
> Created a new atom named: 2H2 within residue: .R<GRA 4>
>
> Created a new atom named: 3H2 within residue: .R<GRA 4>
>
> Creating new UNIT for residue: GRA sequence: 5
>
> Created a new atom named: C1 within residue: .R<GRA 5>
>
> Created a new atom named: H30 within residue: .R<GRA 5>
>
> Created a new atom named: C2 within residue: .R<GRA 5>
>
> Created a new atom named: H29 within residue: .R<GRA 5>
>
> Created a new atom named: C3 within residue: .R<GRA 5>
>
> Created a new atom named: C4 within residue: .R<GRA 5>
>
> Created a new atom named: C5 within residue: .R<GRA 5>
>
> Created a new atom named: C6 within residue: .R<GRA 5>
>
> .
>
> .
>
> .
>
> .
>
> Created a new atom named: C79 within residue: .R<GRA 5>
>
> Created a new atom named: H36 within residue: .R<GRA 5>
>
> Created a new atom named: 1HH within residue: .R<GRA 5>
>
> Created a new atom named: H8 within residue: .R<GRA 5>
>
> Created a new atom named: H9 within residue: .R<GRA 5>
>
> Created a new atom named: H10 within residue: .R<GRA 5>
>
> Created a new atom named: 2H2 within residue: .R<GRA 5>
>
> Created a new atom named: 3H2 within residue: .R<GRA 5>
>
> Creating new UNIT for residue: GRA sequence: 6
>
> Created a new atom named: C1 within residue: .R<GRA 6>
>
> Created a new atom named: H30 within residue: .R<GRA 6>
>
> Created a new atom named: C2 within residue: .R<GRA 6>
>
> Created a new atom named: H29 within residue: .R<GRA 6>
>
> Created a new atom named: C3 within residue: .R<GRA 6>
>
> Created a new atom named: C4 within residue: .R<GRA 6>
>
> Created a new atom named: C5 within residue: .R<GRA 6>
>
> Created a new atom named: C6 within residue: .R<GRA 6>
>
> Created a new atom named: C49 within residue: .R<GRA 6>
>
> .
> .
> .
> .
> .
>
>
>
> Created a new atom named: 1HH within residue: .R<GRA 7>
>
> Created a new atom named: H8 within residue: .R<GRA 7>
>
> Created a new atom named: H9 within residue: .R<GRA 7>
>
> Created a new atom named: H10 within residue: .R<GRA 7>
>
> Created a new atom named: 2H2 within residue: .R<GRA 7>
>
> Created a new atom named: 3H2 within residue: .R<GRA 7>
>
> Creating new UNIT for residue: GRA sequence: 8
>
> Created a new atom named: C1 within residue: .R<GRA 8>
>
> Created a new atom named: H30 within residue: .R<GRA 8>
>
> Created a new atom named: C2 within residue: .R<GRA 8>
>
> Created a new atom named: H29 within residue: .R<GRA 8>
>
> Created a new atom named: C3 within residue: .R<GRA 8>
>
> Created a new atom named: C4 within residue: .R<GRA 8>
>
> Created a new atom named: C5 within residue: .R<GRA
>
>
> .
>
> .
>
> .
>
> .
>
> Created a new atom named: H8 within residue: .R<GRA 8>
>
> Created a new atom named: H9 within residue: .R<GRA 8>
>
> Created a new atom named: H10 within residue: .R<GRA 8>
>
> Created a new atom named: 2H2 within residue: .R<GRA 8>
>
> Created a new atom named: 3H2 within residue: .R<GRA 8>
>
> Creating new UNIT for residue: PCB sequence: 9
>
> Created a new atom named: O2 within residue: .R<PCB 9>
>
> Created a new atom named: O3 within residue: .R<PCB 9>
>
> Created a new atom named: C2 within residue: .R<PCB 9>
>
> Created a new atom named: C1 within residue: .R<PCB 9>
>
> Created a new atom named: C3 within residue: .R<PCB 9>
>
> Created a new atom named: H3 within residue: .R<PCB 9>
>
> .
> .
> .
> .
> .
>
> Created a new atom named: H6 within residue: .R<PCB 9>
>
> Created a new atom named: H4 within residue: .R<PCB 9>
>
> Created a new atom named: H5 within residue: .R<PCB 9>
>
> Created a new atom named: O1 within residue: .R<PCB 9>
>
> Creating new UNIT for residue: PCA sequence: 10
>
> Created a new atom named: O2 within residue: .R<PCA 10>
>
> Created a new atom named: O3 within residue: .R<PCA 10>
>
> Created a new atom named: C2 within residue: .R<PCA 10>
>
> Created a new atom named: C1 within residue: .R<PCA 10>
>
> Created a new atom named: C3 within residue: .R<PCA 10>
>
> Created a new atom named: H2 within residue: .R<PCA 10>
>
> .
> .
> .
> .
>
> Created a new atom named: H1 within residue: .R<ECA 45>
>
> Created a new atom named: H3 within residue: .R<ECA 45>
>
> Created a new atom named: O1 within residue: .R<ECA 45>
>
> Creating new UNIT for residue: ECA sequence: 46
>
> Created a new atom named: O2 within residue: .R<ECA 46>
>
> Created a new atom named: C3 within residue: .R<ECA 46>
>
> Created a new atom named: C2 within residue: .R<ECA 46>
>
> Created a new atom named: O3 within residue: .R<ECA 46>
>
> Created a new atom named: C1 within residue: .R<ECA 46>
>
> Created a new atom named: H2 within residue: .R<ECA 46>
>
> Created a new atom named: H4 within residue: .R<ECA 46>
>
> Created a new atom named: H1 within residue: .R<ECA 46>
>
> Created a new atom named: H3 within residue: .R<ECA 46>
>
> Created a new atom named: O1 within residue: .R<ECA 46>
>
> Creating new UNIT for residue: ECA sequence: 47
>
> Created a new atom named: O2 within residue: .R<ECA 47>
>
> Created a new atom named: C3 within residue: .R<ECA 47>
>
> Created a new atom named: C2 within residue: .R<ECA 47>
>
> Created a new atom named: O3 within residue: .R<ECA 47>
>
> Created a new atom named: C1 within residue: .R<ECA 47>
>
> Created a new atom named: H2 within residue: .R<ECA 47>
>
> .
> .
> .
> .
>
> Created a new atom named: H4 within residue: .R<ECA 59>
>
> Created a new atom named: H1 within residue: .R<ECA 59>
>
> Created a new atom named: H3 within residue: .R<ECA 59>
>
> Created a new atom named: O1 within residue: .R<ECA 59>
>
> Creating new UNIT for residue: PF6 sequence: 60
>
> Created a new atom named: P1 within residue: .R<PF6 60>
>
> Created a new atom named: F1 within residue: .R<PF6 60>
>
> Created a new atom named: F2 within residue: .R<PF6 60>
>
> Created a new atom named: F3 within residue: .R<PF6 60>
>
> Created a new atom named: F4 within residue: .R<PF6 60>
>
> Created a new atom named: F5 within residue: .R<PF6 60>
>
> Created a new atom named: F6 within residue: .R<PF6 60>
>
> Creating new UNIT for residue: PF6 sequence: 61
>
> Created a new atom named: P1 within residue: .R<PF6 61>
>
> Created a new atom named: F1 within residue: .R<PF6 61>
>
> Created a new atom named: F2 within residue: .R<PF6 61>
>
> Created a new atom named: F3 within residue: .R<PF6 61>
>
> Created a new atom named: F4 within residue: .R<PF6 61>
>
> Created a new atom named: F5 within residue: .R<PF6 61>
>
> Created a new atom named: F6 within residue: .R<PF6 61>
>
> Creating new UNIT for residue: PF6 sequence: 62
>
> Created a new atom named: P1 within residue: .R<PF6 62>
>
> Created a new atom named: F1 within residue: .R<PF6 62>
>
> Created a new atom named: F2 within residue: .R<PF6 62>
>
> Created a new atom named: F3 within residue: .R<PF6 62>
>
> Created a new atom named: F4 within residue: .R<PF6 62>
>
> Created a new atom named: F5 within residue: .R<PF6 62>
>
> Created a new atom named: F6 within residue: .R<PF6 62>
>
> Creating new UNIT for residue: PF6 sequence: 63
>
> Created a new atom named: P1 within residue: .R<PF6 63>
>
> Created a new atom named: F1 within residue: .R<PF6 63>
>
> Created a new atom named: F2 within residue: .R<PF6 63>
>
> Created a new atom named: F3 within residue: .R<PF6 63>
>
> Created a new atom named: F4 within residue: .R<PF6 63>
>
> Created a new atom named: F5 within residue: .R<PF6 63>
>
> Created a new atom named: F6 within residue: .R<PF6 63>
>
> .
> .
> .
> .
> .
>
> total atoms in file: 5270
>
> The file contained 4770 atoms not in residue templates
>
> > PCA=loadmol2 PCA_test.mol2
>
> Loading Mol2 file: ./PCA_test.mol2
>
> Reading MOLECULE named PCA
>
> > loadamberparams PCA.frcmod
>
> Loading parameters: ./PCA.frcmod
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> remark goes here
>
> > PCB=loadmol2 PCB_test.mol2
>
> Loading Mol2 file: ./PCB_test.mol2
>
> Reading MOLECULE named PCB
>
> > loadamberparams PCB.frcmod
>
> Loading parameters: ./PCB.frcmod
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> remark goes here
>
> > ECA=loadmol2 ECA_test.mol2
>
> Loading Mol2 file: ./ECA_test.mol2
>
> Reading MOLECULE named ECA
>
> > loadamberparams PCB.frcmod
>
> Loading parameters: ./PCB.frcmod
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> remark goes here
>
> > GRA=loadmol2 gra_test.mol2
>
> Loading Mol2 file: ./gra_test.mol2
>
> Reading MOLECULE named min2.pdb
>
> > loadamberparams GRA.frcmod
>
> Loading parameters: ./GRA.frcmod
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> remark goes here
>
> > PF6=loadmol2 PF6.mol2
>
> Loading Mol2 file: ./PF6.mol2
>
> Reading MOLECULE named PF6
>
> > loadamberparams PF6.frcmod
>
> Loading parameters: ./PF6.frcmod
>
> Reading force field modification type file (frcmod)
>
> Reading title:
>
> remark goes here
>
> > saveamberparm dmin_res dmin_res.prmtop
>
>
> Checking Unit.
>
> WARNING: The unperturbed charge of the unit: 20.000000 is not zero.
>
> FATAL: Atom .R<GRA 1>.A<C1 1> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H30 2> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C2 3> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H29 4> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C3 5> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C4 6> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C5 7> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C6 8> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C49 9> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C50 10> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<3HH 11> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C51 12> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<1H1 13> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C52 14> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C53 15> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C54 16> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C58 17> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C10 18> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C9 19> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C8 20> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C7 21> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C36 22> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C35 23> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C33 24> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C34 25> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H28 26> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<CC1 27> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H27 28> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H26 29> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H25 30> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H24 31> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C37 32> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C38 33> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C11 34> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C12 35> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C13 36> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C14 37> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C62 38> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C57 39> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C56 40> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C55 41> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C90 42> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C86 43> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C81 44> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C82 45> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<2H1 46> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C83 47> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H34 48> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C84 49> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C85 50> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C87 51> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C88 52> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C89 53> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C94 54> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C59 55> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C60 56> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C61 57> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C66 58> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C18 59> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C17 60> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C16 61> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C15 62> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C40 63> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C39 64> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<2HH 65> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<3H1 66> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C41 67> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C42 68> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C19 69> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C20 70> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C21 71> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C22 72> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C70 73> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C65 74> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C64 75> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C63 76> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C98 77> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C93 78> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C92 79> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C91 80> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H35 81> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H1 82> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H2 83> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H3 84> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H4 85> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H5 86> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C95 87> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C96 88> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C97 89> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C67 90> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C68 91> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C69 92> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C74 93> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C26 94> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C25 95> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C24 96> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C23 97> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C44 98> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C43 99> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<1H2 100> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C47 101> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C48 102> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C31 103> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H16 104> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H17 105> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H18 106> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H19 107> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H20 108> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C45 109> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C46 110> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C27 111> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C28 112> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C29 113> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C32 114> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C80 115> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C77 116> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H14 117> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H15 118> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C30 119> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C78 120> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C73 121> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C72 122> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C71 123> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C99 124> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H6 125> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H7 126> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C75 127> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C76 128> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<C79 129> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H36 130> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<1HH 131> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H8 132> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H9 133> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<H10 134> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<2H2 135> does not have a type.
>
> FATAL: Atom .R<GRA 1>.A<3H2 136> does not have a type.
>
> .
> .
> .
> .
>
> FATAL: Atom .R<PCB 9>.A<O2 1> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<O3 2> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<C2 3> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<C1 4> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<C3 5> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<H3 6> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<H2 7> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<H1 8> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<C4 9> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<H6 10> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<H4 11> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<H5 12> does not have a type.
>
> FATAL: Atom .R<PCB 9>.A<O1 13> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<O2 1> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<O3 2> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<C2 3> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<C1 4> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<C3 5> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<H2 6> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<H3 7> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<O1 8> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<H1 9> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<C4 10> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<H6 11> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<H5 12> does not have a type.
>
> FATAL: Atom .R<PCA 10>.A<H4 13> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<O2 1> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<O3 2> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<C2 3> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<C1 4> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<C3 5> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<H3 6> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<H2 7> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<H1 8> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<C4 9> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<H6 10> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<H4 11> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<H5 12> does not have a type.
>
> FATAL: Atom .R<PCB 11>.A<O1 13> does not have a type.
>
> .
>
> .
>
> .
>
> .
>
> .
>
> FATAL: Atom .R<ECA 33>.A<O2 1> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<C3 2> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<C2 3> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<O3 4> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<C1 5> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<H2 6> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<H4 7> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<H1 8> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<H3 9> does not have a type.
>
> FATAL: Atom .R<ECA 33>.A<O1 10> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<O2 1> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<C3 2> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<C2 3> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<O3 4> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<C1 5> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<H2 6> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<H4 7> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<H1 8> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<H3 9> does not have a type.
>
> FATAL: Atom .R<ECA 34>.A<O1 10> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<O2 1> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<C3 2> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<C2 3> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<O3 4> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<C1 5> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<H2 6> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<H4 7> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<H1 8> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<H3 9> does not have a type.
>
> FATAL: Atom .R<ECA 35>.A<O1 10> does not have a type.
>
> .
>
> .
>
> .
>
> .
>
> Failed to generate parameters
>
> Parameter file was not saved.
>
>
>
>
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Ask yourselves, all of you, what power would hell have if those imprisoned
here could not dream of heaven?
_______________________________________________
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Received on Fri Jul 10 2015 - 14:00:04 PDT
