AMBER Archive (2004)

Subject: RE: AMBER: add Na+

From: L Jin (s0344557_at_sms.ed.ac.uk)
Date: Wed Feb 25 2004 - 04:33:02 CST

Bill,

Thank you for reply. Now I realize that I do not need to run antechamber. I just
need to add 3 Na+ into my molecule and then save parm files for future use. But
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+

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.

Lan

Quoting Bill Ross <ross_at_cgl.ucsf.edu>:

> > Now I have got 3 visible Na+. But when I ran antechamber
>
> Why are you running antechamber?
>
> Bill
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