On Fri, Feb 01, 2013, Joe Passman wrote:
>
> 'ATOMS DO NO MATCH BETWEEN PARM AND MIN FILES 1205568 120556'.
Your prmtop appears to have more than more than 1 million atoms. I'm a little
fuzzy on how much of Amber has been upgraded to handle such systems, but
ambpdb is certainly one of the programs that can't, since it only looks at the
first six columns of the second line of the coordinate file to determine the
number of atoms.
For some time, developers resisted allowing systems with more than a million
atoms, on the theory that (at least with Amber) there really isn't anything
interesting you can learn from such a system, since simulations at that size
would be so slow as to not be able to move very far away from their starting
points. The some competitive folks said "if NAMD can do this, we have to be
able to do it as well", and at least some support was added for these large
systems, but (as you have found) it is not universal, and certainly not well
tested.
Bottom line: running these gigantic systems is not for the beginner or for the
faint of heart. And I don't think anything like these sizes are needed to
study conformational fluctuations in a peptide.
...dac
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Received on Fri Feb 01 2013 - 19:00:03 PST
