On Wed, Apr 13, 2011 at 4:33 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
> Thanks, Jason.
> Manual addition of the box flag resolved the previous issue, but pmemd
> complained about the lack of ATOMS_PER_MOLECULE records in the prmtop
>
Ah, I didn't realize that your prmtop file didn't have ATOMS_PER_MOLECULE.
That's certainly necessary. Wrapping/imaging is done based on that, as well
as pressure scaling. I would suggest following Bud Dodson's advice, as I
believe he has a bit of experience with packmol --> amber (you can check the
archive for his contributions to that effect!). My comments/suggestions are
borne completely out of my experience with the sander code and topology file
formats, not any practical hands-on experience with packmol (even though
I've suggested it as a tool in the past ;) ).
All the best,
Jason
file. So I just reran tleap with setbox command, and everything was
> taken care of. Only needed to manually correct the solvent start index
> to make sure that both octanol and water are treated as solvent.
>
> Thanks again for your help
>
> Sasha
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Wed Apr 13 2011 - 17:00:04 PDT
