>Oooh, this is a *big* molecule. You will probably have to break it into
>fragments.
>SQM is trying to geometry optimize this molecule to a very high
>geometrical tolerance, which could take more or less forever. You might
>try to drastically relax the geometry tolerance, but examing carefully the
>resulting atom types and charges. Better is to split the system into many
>smaller fragments (I know: not an easy task).
Splitting it into fragments seems to me that it would defeat the purpose of
what I am trying to do (i.e. there might be hydrogen bonding between
fragments). Even if the ending step is to "stitch" the molecule back
together, it seems very complicated, so I'll try to come up with a few
solutions and only do this as a last resort.
What I am trying to do is create the .prmtop and .inpcrd of a molecule of
interest so I can input them into the OpenMM API. *That is my only goal, I
do not care about that pathway to get there.* I do not (think) that I need
the molecule to be geometrically optimized (maybe there is a flag I can put
to ignore that step if it is nonvital?)
What I do is create the molecule in PyMol and save it as a .pdb, then use
antechamber and tleap to make the target files.
I have tried to skip this pdb > mol2 conversion to avoid this sqm step by
saving as .mol2 in PyMol and Spartan'08.
PyMol's .mol2 was completely incompatible but Spartan's seems more so, I
get this error while loading into tleap: http://pastebin.com/34ZU0yQx
Perhaps I could even build the molecule inside of AMBER somehow (google
search yielded nothing) and save it as .mol2?
Any suggestions would help, and as always thank you David for your time :)
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Received on Mon Feb 04 2013 - 22:00:02 PST
