AMBER Archive (2008)

Subject: RE: AMBER: igb and ibelly

From: Holly Freedman (freedman_at_phys.ualberta.ca)
Date: Fri May 30 2008 - 15:21:06 CDT

Hi Ross,
Thanks a lot. I'll let you know how this works for me.
Holly

> Hi Holly,
>
> The code to do it is missing. GB calculations use a completely different
> code branch in sander than do PME or vacuum calculations. I think you can
> use belly with GB as long as you only fix the last atoms. I.e. a continuous
> set of atoms that includes the last one (or perhaps it is the first) I
> forget. I did fix the code at some point to allow ibelly to be used with GB
> for an arbitrary set of atoms. I think it was against some version of AMBER
> 9 but I don't recall if it was the released version or a specific
> development version.
>
> Anyway, you can try the attached patch against amber 9 and see what happens.
> Beware that the reason this never made it into the main code tree was
> because I didn't have the time to actually check that it was correct, gave
> the correct answer etc. So caveat emptor...
>
> All the best
> Ross
>
> > -----Original Message-----
> > From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf
> > Of Holly Freedman
> > Sent: Friday, May 30, 2008 12:23 PM
> > To: amber_at_scripps.edu
> > Subject: AMBER: igb and ibelly
> >
> > Dear AMBER help,
> > Can someone please explain to me why it is that the ibelly option is not
> > allowed with igb>0
> > (Generalized Born)? I don't understand how the two options are connected.
> > Holly
> >
> > --
> > Department of Physics, University of Alberta
> > Edmonton CANADA
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--
Department of Physics, University of Alberta
Edmonton CANADA

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