AMBER: Fwd: antechamber save prmtop inpcrd

From: Francesco Pietra <>
Date: Tue, 3 Jul 2007 23:14:23 -0700 (PDT)

Warning "not saved" on quitting xleap after having run

saveamberparm ...

is typical behavior of xleap (I have run this command again with the
sustiva-antechamber tutorial). Please disregard my question below.


--- Francesco Pietra <> wrote:

> Date: Tue, 3 Jul 2007 10:55:11 -0700 (PDT)
> From: Francesco Pietra <>
> Subject: antechamber save prmtop inpcrd
> To: Amber <>
> 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
> 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
> Don't pick lemons.
> See all the new 2007 cars at Yahoo! Autos.

Get the free Yahoo! toolbar and rest assured with the added security of spyware protection.
The AMBER Mail Reflector
To post, send mail to
To unsubscribe, send "unsubscribe amber" to
Received on Sun Jul 08 2007 - 06:07:03 PDT
Custom Search