Dear Dr. Jason,
I have used the following command for amber10 earlier and it worked
successfully for other ligands.
antechamber -i VD69.pdb -fi pdb -o VD69_1.prep -fo prepi -c bcc -s 2
But the same set of commands for this ligand (VD69) gave the following error
in amber11. (This error did not appear when I used am1bcc in place of bcc in
amber11)
Please check the attached sqm.out file for details of failure with bcc in
amber11.
Thank you
Error
-----
[vaibhav.localhost VD69]$ antechamber -i VD69.pdb -fi pdb -o VD69_1.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
-----
On Wed, Aug 24, 2011 at 8:53 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Wed, Aug 24, 2011, vaibhav dixit wrote:
>
> > In the meanwhile, I have used am1bcc in place of bcc, which has worked.
>
> Can you be more explicit? Exactly where did you replace "bcc" with
> "am1bcc"?
> Which one was amber10 and which amber11? What were the errors (e.g. in the
> sqm.out file) for the run that failed?
>
> > If yes, then is it reasonable to stick to the original geometry instead
> of
> > trying to minimize.
>
> The am1-bcc (i.e. the "-c bcc" flag to antechamber) charge model
> is supposed to use an AM1 minimized geometry. In principle, you could
> modify
> the sqm.in file (or use the -ek flag to antechamber) to avoid
> minimization,
> but that would in effect be a different charge model. And, if you do have
> a
> funny input geometry, it might lead to odd results.
>
> ....dac
>
>
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>
--
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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- application/octet-stream attachment: sqm.out
Received on Thu Aug 25 2011 - 01:30:02 PDT
