Hi,
This behavior has been observed before, and I believe it's because SQM
has a more strict convergence criterion compared to the older MOPAC.
From the AmberTools manual:
"By default, the AM1 Mulliken charges that are required for the
AM1-BCC procedure are
computed using the sqm program, with the following keyword (which is
placed inside the
&qmmm namelist):
qm_theory=’AM1’, grms_tol=0.0002, tight_p_conv=1, scfconv=1.d-10,
For some molecules, especially if they have bad starting geometries,
convergence to these
tight criteria may not be obtained. If you have trouble, examine the
sqm.out file, and try
changing scfconv to 1.d-8 and/or tight_p_conv to 0. You may also need
to increase the
value of grms_tol. You can use the -ek flag to antechamber to change
these, or just
manually edit the sqm.in file. But be aware that there may be something
“wrong” with
your molecule if these problems arise; the acdoctor program may help."
Hope this is helpful.
-Dan
On Thu, Aug 25, 2011 at 4:15 AM, vaibhav dixit <vaibhavadixit.gmail.com> wrote:
> 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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>> 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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>
>
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Received on Thu Aug 25 2011 - 04:30:03 PDT
