On Sat, Jan 28, 2012, Maryam Hamzehee wrote:
> I used the
> following command:
> $AMBERHOME/exe/sander
> -O -i sasa.in -p dof1_na_solvated.prmtop -c dof1_na_solvated.inpcrd -x
> prod1.mdcrd -o SASA.out
>
> sasa.in
> &cntrl
> imin = 5,
> restraintmask=':1-73'
> #mask =
> :1-73
> /
> &gb
> gbsa = 1,
> surften = 1
> /
The above is way wrong: the lines beginning with "#mask" and ":1-73" should
be removed; further, there is no "gb" namelist: put gbsa and surften into
the cntrl namelist.
But better, wait to see if the cpptraj problem has an easy solution. It kind
of looks like you have a bad (zero) value for the probe radius(?)
....dac
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Received on Sat Jan 28 2012 - 07:00:03 PST
