AMBER Archive (2009)

Subject: [AMBER] FATAL error in creating topology and coordinate files for organic molecules with Antechamber

From: Workalemhu Berhanu (wberhanu_at_mail.ucf.edu)
Date: Tue May 26 2009 - 16:45:55 CDT

Dear all
Hi
I created the pdb file after doing the optimizing the geometry and calculation the electrostatic potential in Gaussian. I use gauss view and saved as mol2 file and open it in viewer Lite and saved it as pdb file. When I followed the steps in the tutorial 4 for creating topology and coordinate files for my molecule I got the result below. Can I get an advice what to do with my molecules (it is an organic conjugated system which some aromatic rings) and it has a charge of one. I thank you in advance
With regards
Workalemahu

$AMBERHOME/exe/antechamber -i MyrcetinHFC.pdb -fi pdb -o MyrcetinHFC.mol2 -fo mol2 -c bcc -s 2
Running: /home/wberhanu/amber9/exe/bondtype -i ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full

Running: /home/wberhanu/amber9/exe/atomtype -i ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff

Total number of electrons: 164; net charge: 0

Running: $AMBERHOME/exe/divcon

Running: /home/wberhanu/amber9/exe/am1bcc -i ANTECHAMBER_AM1BCC_PRE.AC -o ANTECHAMBER_AM1BCC.AC -f ac -p /home/wberhanu/amber9/dat/antechamber/BCCPARM.DAT -s 2 -j 1

Running: /home/wberhanu/amber9/exe/atomtype -f ac -p bcc -o ANTECHAMBER_AM1BCC.AC -i ANTECHAMBER_AM1BCC_PRE.AC
MRE=loadmol2 MyrcetinHFC.mol2
Loading Mol2 file: ./MyrcetinHFC.mol2
Reading MOLECULE named MOL
edit MRE
MRE=loadmol2 MyrcetinHFC.mol2
Loading Mol2 file: ./MyrcetinHFC.mol2
Reading MOLECULE named MOL
> edit MRE
> loadamperparams MyrcetinHFC.frcmod
loadamberparams MyrcetinHFC.frcmod
Loading parameters: ./MyrcetinHFC.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
model = loadpdb "MyrcetinHFC.pdb"
Created a new atom named: C10 within residue: .R<MOL 1>
Created a new atom named: H11 within residue: .R<MOL 1>
Created a new atom named: O12 within residue: .R<MOL 1>
Created a new atom named: H13 within residue: .R<MOL 1>
Created a new atom named: C14 within residue: .R<MOL 1>
Created a new atom named: C15 within residue: .R<MOL 1>
Created a new atom named: C16 within residue: .R<MOL 1>
Created a new atom named: C17 within residue: .R<MOL 1>
Created a new atom named: C18 within residue: .R<MOL 1>
Created a new atom named: C19 within residue: .R<MOL 1>
Created a new atom named: O20 within residue: .R<MOL 1>
Created a new atom named: O21 within residue: .R<MOL 1>
Created a new atom named: O22 within residue: .R<MOL 1>
Created a new atom named: H23 within residue: .R<MOL 1>
Created a new atom named: O24 within residue: .R<MOL 1>
Created a new atom named: O25 within residue: .R<MOL 1>
Created a new atom named: H26 within residue: .R<MOL 1>
Created a new atom named: O27 within residue: .R<MOL 1>
Created a new atom named: H28 within residue: .R<MOL 1>
Created a new atom named: H29 within residue: .R<MOL 1>
Created a new atom named: H30 within residue: .R<MOL 1>
Created a new atom named: H31 within residue: .R<MOL 1>
Created a new atom named: H32 within residue: .R<MOL 1>
Created a new atom named: H33 within residue: .R<MOL 1>
  total atoms in file: 33
  The file contained 33 atoms not in residue templates
saveamberparm model MYRC_vac.prmtop MYRC_vac.inpcrd
FATAL: Atom .R<MOL 1>.A<C10 10> does not have a type.
FATAL: Atom .R<MOL 1>.A<H11 11> does not have a type.
FATAL: Atom .R<MOL 1>.A<O12 12> does not have a type.
FATAL: Atom .R<MOL 1>.A<H13 13> does not have a type.
FATAL: Atom .R<MOL 1>.A<C14 14> does not have a type.
FATAL: Atom .R<MOL 1>.A<C15 15> does not have a type.
FATAL: Atom .R<MOL 1>.A<C16 16> does not have a type.
FATAL: Atom .R<MOL 1>.A<C17 17> does not have a type.
FATAL: Atom .R<MOL 1>.A<C18 18> does not have a type.
FATAL: Atom .R<MOL 1>.A<C19 19> does not have a type.
FATAL: Atom .R<MOL 1>.A<O20 20> does not have a type.
FATAL: Atom .R<MOL 1>.A<O21 21> does not have a type.
FATAL: Atom .R<MOL 1>.A<O22 22> does not have a type.
FATAL: Atom .R<MOL 1>.A<H23 23> does not have a type.
FATAL: Atom .R<MOL 1>.A<O24 24> does not have a type.
FATAL: Atom .R<MOL 1>.A<O25 25> does not have a type.
FATAL: Atom .R<MOL 1>.A<H26 26> does not have a type.
FATAL: Atom .R<MOL 1>.A<O27 27> does not have a type.
FATAL: Atom .R<MOL 1>.A<H28 28> does not have a type.
FATAL: Atom .R<MOL 1>.A<H29 29> does not have a type.
FATAL: Atom .R<MOL 1>.A<H30 30> does not have a type.
FATAL: Atom .R<MOL 1>.A<H31 31> does not have a type.
FATAL: Atom .R<MOL 1>.A<H32 32> does not have a type.
FATAL: Atom .R<MOL 1>.A<H33 33> does not have a type.
Failed to generate parameters
Parameter file was not saved.

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