Dear David,
Thanks for helping me out here because I am quite lost in how to fix the
problem for the moment. There is clearly something going wrong with the
extra points but I am not quite sure why this is added or when it is added.
I have done some further testing where instead of the octahedral geometry I
generate a minimal version of this geometry where no atom type is redundant
- essentially removed all opposite atoms such that I do not have any of the
180 degrees angles between the atoms/dummy atoms. When I minimize this I
have not problems and it minimizes fine.
When I add one more dummy atoms to the complex I get the errors again with
EXTRA POINTS: nnb too small!
nnb,ntot = 11 29
attached are the files to generate ( debug.frcmod, debug.pdb, debug.lib )
I have also attached the files used to generate the octahedral complex (
octa.frcmod, octa.lib ).
I am not quite sure which files to start debugging for the extra points so
any advise would be very helpful
Thanks
On Mon, Dec 1, 2014 at 4:24 AM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Nov 30, 2014, Jorgen Simonsen wrote:
> >
> > Sorry for the missing information - so I am trying to create an
> octahedral
> > geometry with six point charge around the main atom.
>
> > EXTRA POINTS: nnb too small!
> > nnb,ntot = 22 60
>
> It's not clear from your description that you even *have* extra points. Do
> the names of your atoms begin with "EP"?
>
> >
> > I am not quite sure how to fix this appropriately. I looked at the code
> for
> > extra_pts.F90 I tried to treat the points as regular atoms but same crash
> > as above.
>
> Again, email is a hard medium to discuss these sorts of problems. We only
> know a bit about what you did: for example, what changed when you "tried to
> treat the points as regular atoms"? The error is still in the extra points
> code, so you must not have been successful in doing that.
>
> > I also tried the frameon=1 but resulted in a new error:
> >
> > namelist read: missplaced = sign
> > Cannot match namelist object name 1,
> >
> > so the key word is not recognized as input.
>
> This is not usually the error that would be given if the keyword were not
> recognized. "misplaced = sign" suggests some other syntax problem.
> Be sure that frameon is in the &ewald namelist. But also note that
> frameon=1
> is the default, so it's not clear that adding this will have any effect.
>
> To be sure, it's pretty hard indeed to make an octahedral system in Amber.
> You are probably going to have to solve most of this yourself, by adding
> debugging print statements or other means. You might start by tracing down
> why you are getting extra point errors when you are trying to have no extra
> points.
>
> ....dac
>
>
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Received on Mon Dec 01 2014 - 15:30:03 PST
