On Fri, Apr 10, 2015 at 6:23 PM, Sofia Vasilakaki <svasilak.chem.uoa.gr>
wrote:
> Thank you for your reply,
>
> I have tried use_sander=1 using 4 frames but I got the same error. I have
> boundary conditions and this may cause problems (although I have run nmode
> in other proteins with periodic boundaries and there was no problem) so Ι
> used cpptraj and nobox to built prmtops but no results. My system is
> 132,866 atoms.
>
use_sander has no effect on normal mode calculations.
The fact that you have 132,866 atoms in your system and the first error
message you got said something like:
Second derivatives are not supported for periodic systems; exiting.
leads me to believe that you are trying to get a normal mode entropy
estimate for your explicitly solvated system. If your system has a lot of
waters and you're trying to compute an entropy using normal mode analysis,
then it suggests to me that you don't really understand what the normal
mode approximation *is* and how it can be used. You need to gain that
understanding before you try to use it. What you are trying to do will not
work, nor is that a type of problem that the normal mode approximation was
designed to address.
The heart of the normal mode approximation is the rigid rotor model (which
isn't really accurate for a squishy biomolecule and is *definitely* wrong
for a biomolecule solvated in a microscopic water droplet). I suggest
looking at the MMPBSA.py citation and looking at the normal mode section
there (which I believe has more citations if you need them). For example:
http://www.sciencedirect.com/science/article/pii/S1093326304000476
and
http://pubs.acs.org/doi/abs/10.1021/ja981844%2B
On the other hand, if your system does *not* have explicit solvent, and it
really *does* have over 100,000 atoms, the likelihood of normal mode
analysis working (i.e., providing useful information) is probably very low.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sat Apr 11 2015 - 21:00:02 PDT
