Dear David,
Sorry for the missing information - so I am trying to create an octahedral
geometry with six point charge around the main atom.
So I have create a library file through xleap with six dummy atom DD1-DD6
where DD1 and DD4 is the same type such that it forms two triangles.
I have named the dummy atoms DD1-DD6 and made bonds such that all dummy
atoms are connected to the main atom and the rest are interconnected in the
following way in the library file:
!entry.ZNA.unit.connectivity table int atom1x int atom2x int flags
1 2 1
1 3 1
1 4 1
1 5 1
1 6 1
1 7 1
2 3 1
2 4 1
2 6 1
2 7 1
3 4 1
3 5 1
3 7 1
4 5 1
4 6 1
5 6 1
5 7 1
6 7 1
mirror atoms are not connected directly e.g. 2-5, 3-6, 4-7. All torsion
angles are set to zero in the parameter file for the complex.
I get a lot of warning when I built the complex - this one I ignore:
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X ZN D2-X 0.0 180. 2.
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X ZN D3-X 0.0 180. 2.
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X ZN D4-X 0.0 180. 2.
WARNING: expected Improper Torsion PK>0 (0.000000)
Here is the Improper Torsion line in question:
X D2 D3-X 0.0 180. 2.
WARNING: expected Improper Torsion PK>0 (0.000000)
Next warning is this
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-DD6-DD7-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-DD5-DD6-*
+--- With Sp0 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-DD5-DD7-*
+--- With Sp0 - Sp0
which I also ignore and for building the torsions I get the following
warning:
1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 6 7 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 5 6 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 5 7 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 5 7 duplicates bond ('triangular' bond) or angle ('square' bond)
1-4: angle 5 6 duplicates bond ('triangular' bond) or angle ('square' bond)
which is correct but as I understand I do want to have a triangular bond.
It generates the parameter and topology file for the complex and then I get
the error trying to test the parameters:
With the initial parameters I get the following error when trying to do a
minimization
“”"
Minimization of complex
&cntrl
imin = 1,
maxcyc = 10000,
ntb = 0,
cut = 10.0
/
“”"
Energy minimization:
maxcyc = 10000, ncyc = 10, ntmin = 1
dx0 = 0.01000, drms = 0.00010
EXTRA POINTS: nnb too small!
nnb,ntot = 22 60
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. The dummy atoms have been given a low weight and vdw parameters
(3.0 and vdw = 0.050 & 0.00). 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. Any suggestions to how to fix
this would be highly appreciated.
Thanks
On Sun, Nov 30, 2014 at 12:43 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Sun, Nov 30, 2014, Jorgen Simonsen wrote:
> >
> > I am trying to generate a molecule with dummy charges distributed around
> it
> > - but I am getting some problems when I try to minimize it with amber12 :
> >
> > EXTRA POINTS: nnb too small!
> > nnb,ntot = 22 60
>
> It's hard to be of help without more information. It sounds like you are
> trying to use unconventional extra points (i.e designing your own, and not
> using things already in the Amber library.) This requires a (farily deep)
> understanding of how extra points are handled inside the code. The types
> of
> extra points allowed is limited to a small number of options: see the code
> in extra_pts.F90.
>
> ....hope this helps....dac
>
>
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Received on Sun Nov 30 2014 - 15:00:02 PST
