On Fri, Oct 21, 2005, David Mobley wrote:
>
> Then I "cat" leap.log and see the following errors (warnings, really):
> ** Warning: No sp2 improper torsion term for c-ne-cd-cd
> atoms are: C4 N5 C4A C10
> ** Warning: No sp2 improper torsion term for ne-ca-ca-ca
> atoms are: N5 C6 C5A C9A
> ** Warning: No sp2 improper torsion term for ca-ca-ca-ha
> atoms are: C5A C7 C6 H6
> ** Warning: No sp2 improper torsion term for ca-ca-ca-ha
> atoms are: C8 C9A C9 H9
> ** Warning: No sp2 improper torsion term for ca-ca-ca-nh
> atoms are: C5A C9 C9A N10
> ** Warning: No sp2 improper torsion term for ca-cd-nh-c3
> atoms are: C9A C10 N10 C1*
> ** Warning: No sp2 improper torsion term for nc-cd-cd-nh
> atoms are: N1 C4A C10 N10
Amber force field generally leave out improper torsions that connect fused
rings. So four of the above are expected, but the rest are not. Maybe
Junmei has some ideas here(?).
> Note also that this procedure normally works fine for most of the
> small molecules I've tried, but for some reason I'm getting these
> warnings in this case. Further, if I ignore the warnings and go ahead
> and put the molecule in water and minimize, minimization usually exits
> with a segmentation fault after several hundred steps.
It seems unlikely that the two things are connected... what does the structure
look like upon minimization? Do the energies look weird. Amber should not
be segfaulting even in there is a problem with the force field.
....dac
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Received on Fri Oct 21 2005 - 19:53:00 PDT
