AMBER Archive (2009)

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

From: Rubben Torella (rubben.torella_at_gmail.com)
Date: Tue May 26 2009 - 17:33:18 CDT

OK there are two kind of errors: the first proably the pdb you loaded has
diferent atom name respect of the standard atom name considered by leap..
you have to check the pdb in the position leap indicates you...
Then I think you have to put the option -nc (net charge) 1 in the
antechamber operation in order to have the correct charge.
I hope this can help you...

2009/5/26 Workalemhu Berhanu <wberhanu_at_mail.ucf.edu>

> 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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