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
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Received on Wed Aug 24 2011 - 05:00:02 PDT
