AMBER Archive (2007)

Subject: Re: AMBER: refc error

From: David A. Case (case_at_scripps.edu)
Date: Mon Jul 16 2007 - 19:25:20 CDT

On Mon, Jul 16, 2007, Lili Peng wrote:
>
> I am having trouble running a restrained energy minimization on an organic
> molecule. When I try to run it in Sander, I type in:
>
> " $AMBERHOME/exe/sander.1cpu -O -i min1.in -o min1.out -p taxol.prmtop -c
> taxol.inpcrd -r min1.rst "
>
> My min1.in consists of:
>
> " Initial minimization of structure
> &cntrl
> imin=1, maxcyc=200,
> ntpr=10,
> ntr=1,
> ibelly=1,
> bellymask=':1-20',
> /
> "
> However, when I try running the minimization, I get the error:
> " Unit 10 Error on OPEN: refc"
>
> I Googled this problem, and I get some hits about specifying a refc file.
> How do I go about doing so?

Use the "-ref" flag to sander. However, in the above, you will also need
restraintmask and a restraint_wt entries in the cntrl namelist.

We're trying to get rid of "belly" altoghter: unless you are sure that you
need to set ibelly, I would advise not using it. There are a handful of
"expert" places where ibelly=1 is needed, but I haven't used this option
in the last 10 years. Please read carefully the warnings on p. 93 of the
Users' Manual about the ibelly flag. My guess is that the next release of
Amber will not simply rely on warnings in the Users' Manual, but will disable
the feature altogether. Stick with restraints.

....dac

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