Beautiful Jason. Thanks a lot it worked fine.
It wouldn't be the case so for another patch in AmberTools?
Cheers,
Alan
On 18 August 2010 15:12, Jason Swails <jason.swails.gmail.com> wrote:
> Hello,
>
> In the function "gasiter" in charge.c
> ($AMBERHOME/AmberTools/src/antechamber), an integer "total charge" is
> compared to a double "gas charge". This will only work if the total charge
> calculated in the floating point number reaches exactly 3, but it's pretty
> easy to make this fail. For example, using gcc, the result
>
> 3 == 0.0003 * 10000
>
> returns False. Try changing the line
>
> if(TotalGasCharge != netcharge) {
>
> To
>
> if(fabs(TotalGasCharge - (double) netcharge) < 1e-6) {
>
> That should get rid of any minor roundoff error (maybe make the value of
> "0"
> a little smaller if you're worried about a 1 x 10^-6 difference in
> charges).
>
> Good luck!
> Jason
>
> On Wed, Aug 18, 2010 at 4:41 AM, Alan <alanwilter.gmail.com> wrote:
>
> > This a sort of test I am doing and found something bizarre.
> >
> > I have an ARG tri-peptide (NARG-ARG-CARG), but pretend you don't know
> this,
> > and I want to use antechamber to get its topology.
> >
> > BTW, I use tleap to create the peptide and then sander to optimise it.
> >
> > If I do:
> >
> > ------------------------------------------------------------------
> > antechamber -i agRRR.mol2 -fi mol2 -o agRRR_bcc_amber.mol2 -fo mol2 -c
> bcc
> > -nc 3 -m 1 -s 2 -df 2 -at amber -pf n
> >
> > Running: /Users/alan/Programmes/amber11/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > ---Judge bond type for Residue 1 with ID of 1 and Name of ARG ---
> >
> > Info: Bond types are assigned for valence state 1 with penalty of 1
> >
> > ---Judge bond type for Residue 2 with ID of 2 and Name of ARG ---
> >
> > Info: Bond types are assigned for valence state 15 with penalty of 1
> >
> > ---Judge bond type for Residue 3 with ID of 3 and Name of ARG ---
> >
> > Info: Bond types are assigned for valence state 15 with penalty of 1
> >
> > Running: /Users/alan/Programmes/amber11/bin/atomtype -i
> ANTECHAMBER_AC.AC0
> > -o ANTECHAMBER_AC.AC -p amber
> >
> > Total number of electrons: 262; net charge: 3
> >
> > Running: /Users/alan/Programmes/amber11/bin/sqm -O -i sqm.in -o sqm.out
> > ------------------------------------------------------------------
> >
> > Then parmchk and tleap etc.
> >
> > * It works. *
> >
> > But if I want to use Gasteiger charges:
> >
> > ------------------------------------------------------------------
> > antechamber -i agRRR.mol2 -fi mol2 -o agRRR_gas_amber.mol2 -fo mol2 -c
> gas
> > -nc 3 -m 1 -s 2 -df 2 -at amber -pf n
> >
> > Running: /Users/alan/Programmes/amber11/bin/bondtype -j full -i
> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> > ---Judge bond type for Residue 1 with ID of 1 and Name of ARG ---
> >
> > Info: Bond types are assigned for valence state 1 with penalty of 1
> >
> > ---Judge bond type for Residue 2 with ID of 2 and Name of ARG ---
> >
> > Info: Bond types are assigned for valence state 15 with penalty of 1
> >
> > ---Judge bond type for Residue 3 with ID of 3 and Name of ARG ---
> >
> > Info: Bond types are assigned for valence state 15 with penalty of 1
> >
> > Running: /Users/alan/Programmes/amber11/bin/atomtype -i
> ANTECHAMBER_AC.AC0
> > -o ANTECHAMBER_AC.AC -p amber
> >
> > Running: /Users/alan/Programmes/amber11/bin/atomtype -i
> > ANTECHAMBER_GAS.AC-o
> > ANTECHAMBER_GAS_AT.AC -d
> > /Users/alan/Programmes/amber11/dat/antechamber/ATOMTYPE_GAS.DEF
> >
> > The net charge of the molecule (3) does not equal to the total charge
> (3.00
> > ) based on Gasteiger atom type, exit
> > ------------------------------------------------------------------
> >
> > This fails, since file agRRR_gas_amber.mol2 is not generated, so parmchk
> > and
> > tleap will never work.
> >
> >
> > And if I use, for example babel, to get the Gasteiger charges in
> > my agRRR.mol2, and do:
> >
> > antechamber -i agRRR.mol2 -fi mol2 -o agRRR_user_amber.mol2 -fo mol2 -c
> > user
> > -nc 3 -m 1 -s 2 -df 2 -at amber -pf n
> >
> > All works, with a tleap warning about the net charge generated by babel.
> > >From tleap log:
> >
> > ------------------------------------------------------------------
> > [snip]
> > ERROR: The unperturbed charge of the unit: 2.969400 is not integral.
> > WARNING: The unperturbed charge of the unit: 2.969400 is not zero.
> >
> > -- ignoring the error and warning.
> > [snip]
> > ------------------------------------------------------------------
> >
> > But I get the prmtop and inpcrd files in the end.
> >
> > So I am trying to understand why antechamber with gasteiger fails with an
> > incomprehensible error message:
> >
> > "The net charge of the molecule (3) does not equal to the total charge
> > (3.00
> > ) based on Gasteiger atom type, exit"
> >
> > Sounds like I have decimal rounds off problems here?
> >
> > Many thanks,
> >
> > Alan
> > --
> > Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
> > Department of Biochemistry, University of Cambridge.
> > 80 Tennis Court Road, Cambridge CB2 1GA, UK.
> > >>http://www.bio.cam.ac.uk/~awd28 <http://www.bio.cam.ac.uk/%7Eawd28><<
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Alan Wilter S. da Silva, D.Sc. - CCPN Research Associate
Department of Biochemistry, University of Cambridge.
80 Tennis Court Road, Cambridge CB2 1GA, UK.
>>http://www.bio.cam.ac.uk/~awd28<<
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Received on Wed Aug 18 2010 - 09:00:03 PDT
