AMBER Archive (2007)

Subject: AMBER: antechamber save prmtop inpcrd

From: Francesco Pietra (chiendarret_at_yahoo.com)
Date: Tue Jul 03 2007 - 12:55:11 CDT

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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