I run the antechamber-sustiva tutorial successfully with amber9.
Then I applied the same procedure to a novel 98-atoms natural product, the pdb
of which consists of two fragments, following a procedure for calculating RESP
charges via HH/6-31G* (procedure carried out in the past).
Antechamber has encountered only one angle missing from parameters, which was
recalculated by divcon. I have identified on xleap which atoms are involved.
I was actually interested to place the molecule in equilibrated water, so that
I continued as in the tutorial, and the ensemble solute/water looked like fine
(first I tried a 30A box, which added too much water; 10A was OK).
When I saved to get the prmtop and inpcrd files, Files -> Quit of xleap warned
"unsaved". I tried again with the same result, then I quit notwithstanding.
Actually these two requested file exist, 804585 bytes for prmtop and 186198
bytes for inpcrd.
Is that warning a sign of a mistake?
Thanks
francesco pietra
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Received on Wed Jul 04 2007 - 06:07:34 PDT
