Dear Daniel Roe and Yi An,
> I think 150 atoms is much larger than anything antechamber was
> designed to parameterize off the bat. Something like that you would
> typically break down into smaller chemical components and then
> parameterize those (analogous to breaking down a peptide into smaller
> amino acid chunks instead of trying to parameterize the whole thing).
> A good resource for stuff like this is something like R.E.D. server
> (http://q4md-forcefieldtools.org/REDS/).
I think one should always consider splitting a large molecule into
smaller elementary building blocks and generate the corresponding
molecular fragments when one wants to parameterize a large molecule.
R.E.D. and R.E.D. Server are specially designed for this task.
See
http://q4md-forcefieldtools.org/REDDB/projects/F-90/ for instance.
R.E.D. Server at
http://q4md-forcefieldtools.org/REDS/ is limited to
150 atoms.
See
http://q4md-forcefieldtools.org/REDS/faq.php#17; we can obviously
postpone this limit if this is needed by the user; just send a request
to contact_at_q4md-forcefieldtools.org.
R.E.D. Server Development at
http://q4md-forcefieldtools.org/REDS-Development/faq.php#17 is limited
to 350 atoms; This web server handle all the elements of the periodic
tables and is mostly designed for metal complexes. It can be obviously
used for organic molecules but ambiguities between atom names are not
well handled (CA is recognized as a Calcium atom and not as a C alpha
carbon). This is handled within the new R.E.D. version in preparation.
regards, Francois
> On Wed, Oct 31, 2012 at 1:05 PM, Yi An <anyiphysics.gmail.com> wrote:
>> Hi all,
>>
>> I'm now using antechamber to derive partial charges for some large organic
>> molecules. My input file is pdb and I want to get mol2 files for these
>> molecules. My problem is when the molecule contains more than 150 atoms, I
>> can only get the sqm.out file. I can't get the mol2 file even though the
>> sqm.out says the geometry is converged. However, if the molecule has <150
>> atoms then I don't have this problem.
>>
>> The method I use in antechamber is AM1 and the commands are "antechamber -i
>> XXX.pdb -fi pdb -o XXX.mol2 -fo mol2 -c bcc -s 2". Does anyone know if
>> antechamber has a limitation on molecule size? Any related information is
>> appreciated. Thanks.
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Received on Thu Nov 01 2012 - 01:30:03 PDT
