AMBER Archive (2009)

Subject: Re: [AMBER] NAB optimization

From: case (case_at_biomaps.rutgers.edu)
Date: Thu Aug 13 2009 - 08:56:28 CDT

On Thu, Aug 13, 2009, ondrej.prenosil_at_marge.uochb.cas.cz wrote:
>
> we try to optimize in nab, but we do not know how to tell the program to
> write the trajectory or at least the optimized structure.

You can't write a trajectory file during minimization. But you could minimize
for n steps, write out the structure, then repeat.

To save the structure, use setmol_from_xyz() followed by putpdb(); or
you can use the putxv() routine. See Section 10.2 of the Users' Manual for a
simple example.

...dac

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