On Sat, Mar 13, 2010, Workalemhu Berhanu wrote:
> fname_min.in
> initial minimisation prior to MD GB model
> &cntrl
> imin = 1,
> maxcyc = 500,
> ncyc = 250,
> ntb = 0,
> igb = 2
> iamoeba = 1, jfastw=4,
> cut = 12, tautp=5.0,
> /
You can't use gb together with polarizable force fields. (Scott: could you
look into updating mdread.f to flag this incompatibility?)
>
> I also tried to do it in explicit solvent
> I used
> sleap
> source leaprc.amoeba
> COM = loadpdb Peptide.pdb
> charge COM
> solvateoct COM TIP3PBOX 10.
It's likely that amoeba only works with amoeba waters, not with other water
models. Amoeba support in Amber is a specialized code, and you can't just mix
and match the amoeba force field with all the other things that are there.
(Wei: this sort of thing should give a better error message).
...regards...dac
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Received on Sat Mar 13 2010 - 10:00:02 PST
