Dear Dr. Jason and Amber users,
Thank you for that suggestion.
In the meanwhile, I have used am1bcc in place of bcc, which has worked.
Are am1bcc and bcc same and just different commands in amber10 and amber11
for the same charge calculation procedure?
If yes, then is it reasonable to stick to the original geometry instead of
trying to minimize.
(The geometry I'm using has come from a docking experiment where prior
ligand preparation and minimization was done using SYBYL7.1 modules).
Thanks once again.
:)
On Wed, Aug 24, 2011 at 5:22 PM, Jason Swails <jason.swails.gmail.com>wrote:
> Look in sqm.out for the error message (maybe it's a bad starting
> geometry?). You could try optimizing it with some QM software (like
> Gaussian or GAMESS or something) and using that structure in antechamber.
>
> On Wed, Aug 24, 2011 at 12:33 AM, vaibhav dixit <vaibhavadixit.gmail.com
> >wrote:
>
> > Dear Amber users,
> > Thanks for your help and suggestions earlier,
> > I'm getting the following error while using antechamber to generate
> prepin
> > file from pdb file for the ligand. I'm using amber11.
> >
> > The same command was working nicely with amber10. The prepin file is
> > generated correctly if I use other charges like "Gasteiger charges".
> > But I wanted to stick to the bcc charge as I had done for other ligands
> > using amber10.
> > Should the difference in charges (bcc vs gas) affect the result in
> > simulation that I'm going to perform later and calculate free energy
> using
> > MMPBSA?
> >
>
> Yes, it will probably make a difference. At least there's no way to prove
> that it won't unless you use both sets for each ligand. I would imagine
> you'd find it hard to get a mixed-charge-scheme past a reviewer if you
> tried
> comparing the binding free energies of different ligands using different
> charge schemes.
>
> HTH,
> Jason
>
>
> >
> > Errors with antechamber:
> >
> > ----
> > [vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69.prep
> -fo
> > prepi -c bcc -s 2
> > Running: /opt/amber11/bin/bondtype -j full -i ANTECHAMBER_BOND_TYPE.AC0
> -o
> > ANTECHAMBER_BOND_TYPE.AC -f ac
> >
> >
> >
> > Running: /opt/amber11/bin/atomtype -i ANTECHAMBER_AC.AC0 -o
> > ANTECHAMBER_AC.AC -p gaff
> >
> > Total number of electrons: 280; net charge: 0
> >
> > Running: /opt/amber11/bin/sqm -O -i sqm.in -o sqm.out
> > Error: cannot run "/opt/amber11/bin/sqm -O -i sqm.in -o sqm.out" of
> bcc()
> > in
> > charge.c properly, exit
> > ----
> >
> > [vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69.prep
> -fo
> > prepi -c gas (working...)
> >
> >
> > --
> > With regards
> >
> > Vaibhav A. Dixit
> > Ph.D. Scholar
> > Department of Medicinal Chemistry
> > Natl. Inst. Pharm. Edu. & Res. (NIPER)
> > Sector 67, Phase X, S.A.S. Nagar (Mohali)
> > Punjab -160 062 INDIA
> > Phone (Mobile): +919915214408
> > E-mail: vaibhavadixit.gmail.com
> > www.niper.nic.in
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With regards
Vaibhav A. Dixit
Ph.D. Scholar
Department of Medicinal Chemistry
Natl. Inst. Pharm. Edu. & Res. (NIPER)
Sector 67, Phase X, S.A.S. Nagar (Mohali)
Punjab -160 062 INDIA
Phone (Mobile): +919915214408
E-mail: vaibhavadixit.gmail.com
www.niper.nic.in
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Received on Wed Aug 24 2011 - 07:00:03 PDT
