Dear Sir,
Thanks a lot for your useful suggestions. I have the following
doubt,
I have obtained charges from quantum mechanical calculations and it seems
that they work better for my systems. Also I have a decent starting geometry
for the molecule. But how do I create the .mol2 file without running the
SQM. Only if I can create .mol2 file then I can change charges in the file.
After obtaining the .prmtop and .inpcrd file I run a minimization before
going ahead with any other simulations. This should give me a geometry
according the parameters from GAFF. Is this way of preparing the system for
simulation correct.
Also can you elaborate a bit on how to create larger systems from smaller
fragments.
Thanks in advance
with regards,
Chidambar
On Tue, Oct 11, 2011 at 10:48 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Tue, Oct 11, 2011, Chidambar Kulkarni wrote:
>
> > I wanted to know what is the maximum number
> of
> > atoms that can be handled using ANTECHAMBER and SQM. I am asking this
> > question because, I have systems consisting of more than 300 atoms or so
> and
> > moreover I would not successfully create .mol2 file for a system
> containing
> > 192 atoms. Any suggestions on how to handle this will be appreciated.
>
> There is no fixed maximum number. The sqm program is used to compute
> am1-bcc
> charges; if you have another way of getting charges for your system, then
> you
> don't need to use sqm at all.
>
> The am1-bcc procedure, by construction, tries to get an am1-optimized
> geometry
> for your molecule. This can fail if the SCF fails to converge, or if the
> geometry optimization fails to converge. Both are increasingly likely as
> the
> number of atoms grows.
>
> The whole design idea for gaff and am1-bcc was to get automated initial
> guesses for charge and force field models for molecules likely to be
> considered as inhibitors or ligands to proteins. Larger molecules (and
> 300 atoms certainly qualifies), can general be broken into smaller
> fragments, for which force field models can be derived, then reassembled
> to make models for the original, larger system. I hope you can see a way
> to make such a strategy work for your systems.
>
> ...hope this helps...dac
>
>
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>
--
Chidambar k
Int.PhD
JNCASR
Bangalore
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Received on Tue Oct 11 2011 - 21:30:02 PDT
