Re: [AMBER] Problem in charge generation through antechamber

From: ATUL KUMAR <atul44_sit.jnu.ac.in>
Date: Fri, 19 Aug 2016 11:41:14 +0530

Thank you for reply. please find attached pdb file

*Atul Kuamr jaiswal*
Research Scholar
School of Computational and Integrative Sciences
Centre for Computational Biology and Bioinformatics (CCBB)
JNU,New Delhi
India.

On Fri, Aug 19, 2016 at 1:28 AM, Bruno Falcone <brunofalcone.qo.fcen.uba.ar>
wrote:

> It seems that the optimization of the starting structure is not
> converging. Perhaps it's best to first carry out a quick Molecular
> Mechanics optimization of the initial structure. A nice program to do
> this with a GUI is Avogadro, or you could use open-babel.
>
> Are you happy to share the pdb file through here? That could speed up
> the help we can give you,
>
> Cheers,
>
> Bruno
>
> On 18/08/16 16:43, ATUL KUMAR wrote:
> > here is some last lines of sqm.out file
> >
> >
> >
> > ------------------------------------------------------------
> --------------------
> > RESULTS
> > ------------------------------------------------------------
> --------------------
> >
> >
> > QMMM: ERROR!
> > QMMM: Unable to achieve self consistency to the tolerances specified
> > QMMM: No convergence in SCF after 1000 steps.
> > QMMM: E = -0.2388E+07 DeltaE = -0.1360E+04 DeltaP = 0.3567E+00
> > QMMM: Smallest DeltaE = -0.5797E-01 DeltaP = 0.1462E+00 Step = 622
> >
> >
> >
> > *Atul Kuamr jaiswal*
> > Research Scholar
> > School of Computational and Integrative Sciences
> > Centre for Computational Biology and Bioinformatics (CCBB)
> > JNU,New Delhi
> > India.
> >
> > On Fri, Aug 19, 2016 at 1:03 AM, Bruno Falcone <
> brunofalcone.qo.fcen.uba.ar>
> > wrote:
> >
> >> Your command seems OK.
> >>
> >> Check sqm.out, does it give a more informative message? Are you sure the
> >> starting structure is OK?
> >>
> >> Hope this helps,
> >>
> >> Bruno
> >>
> >>
> >> On 18/08/16 15:53, ATUL KUMAR wrote:
> >>> Dear Urers,
> >>> I am using antechamber for generating atomic charges and parameters
> for a
> >>> ligand(Net charge is -4) molecules by the following command:
> >>>
> >>> antechamber -i Mol_red5.pdb -fi pdb -o Mol_red5.mol2 -fo mol2 -c bcc
> -s 2
> >>> -nc -4
> >>>
> >>> after funning this i am getting following error message:
> >>>
> >>> Running: /home/atul_jaiswal/AMBER16/amber16/bin/bondtype -j full -i
> >>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >>>
> >>> Running: /home/atul_jaiswal/AMBER16/amber16/bin/atomtype -i
> >>> ANTECHAMBER_AC.AC0 -o ANTECHAMBER_AC.AC -p gaff
> >>> Total number of electrons: 422; net charge: -4
> >>>
> >>> Running: /home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i sqm.in -o
> >> sqm.out
> >>> Error: cannot run "/home/atul_jaiswal/AMBER16/amber16/bin/sqm -O -i
> >> sqm.in
> >>> -o sqm.out" of bcc() in charge.c properly, exit
> >>>
> >>> Please help me out with this.
> >>>
> >>> *Atul Kuamr jaiswal*
> >>> Research Scholar
> >>> School of Computational and Integrative Sciences
> >>> Centre for Computational Biology and Bioinformatics (CCBB)
> >>> JNU,New Delhi
> >>> India.
> >>> _______________________________________________
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> >>
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Received on Thu Aug 18 2016 - 23:30:02 PDT
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