AMBER Archive (2004)

Subject: RE: AMBER: add Na+

From: Bill Ross (ross_at_cgl.ucsf.edu)
Date: Wed Feb 25 2004 - 12:31:43 CST

> I find it interesting that I can save prmtop and inpcrd files successfully but
> fail in saving the prep file with 'segmentation fault'. And in the
> leap.log the bottom message is just
> > saveAmberPrep MOL "/usr/people/ljin/S-P/TEST/test.prep"
> saving prep, residue MOL
> saving prep, residue Na+

Segmentation fault means bug in the code. It is not a serious
functional problem because the normal use of saveAmberPrep is
to save a single newly-developed residue, not a whole system.
E.g. if you reloaded the prep file, MOL would not include the
ions, since prep format is just for individual residue definitions.

By the way you don't need to use quotes around the file name.

> I used 'addions MOL Na+ 3' to add the 3 Na+. Is the fault because of this
> command line? How can I save all files correctly? Thanks a lot.

The addions line is correct.

If you want to save/reload the whole system, use saveoff/loadoff.

Bill
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