On Wed, Jul 01, 2026, FyD via AMBER wrote:
>
>I do not understand the energy values reported for '3-point' angles in
>triple bonds by sander 2024 (automatic by REDServer Dev./PyRED)|pmemd
>2024; done manually on the q4md-fft and MatriCS
>https://www.matrics.u-picardie.fr/amber/ clusters):
>For HF/6-31G(d) optimized ethyne H-C≡C-H (simple model), there are 2
>angles HCC & CCH, and measured_angle_values ~ parm10 eq. value ~ 180
>deg.; so the corresponding angle energy values ~ 0 kcal/mol:
>sander|pmemd do not find '0'...
The simple force field codes used in Amber cannot handle situations where
the angle is 180: there is no way to compute the force for such an angle.
The force constants for such angles should be zero, at least in my
understanding. You say "sander|pmemd do not find '0'". Is this because
some angles do not have zero force constants? At the very end of your
message, there seem to be some non-zero force constants. Are those in
parm10, or from somewhere else? Do you know what GAFF does it this case?
Others on the list may know more about this issue than I do. One approach
is to include a 1--3 bond (say between H and the second C in ethyne. If the
ideal distance there is the sum of the C--C and C--H bond lengths, it will
serve to keep the angle near 180.
...hope this helps (a little?)....dac
>ParmEd: a Parameter file Editor
>Loaded Amber topology file Data-R.E.D.Server/Mol_MM/MM_sander_vs_pyred_SinglePoint/Mol_mm1-c1.parm7
>Reading input from STDIN...
>>printangle
>printangle command not recognized
>>printangles
> Atom 1 Atom 2 Atom 3 Frc
>Cnst Theta eq
> 1 C1 ( CZ) 3 C2 ( CZ) 4 H2 ( HZ)
>50.0000 180.0001
> 2 H1 ( HZ) 1 C1 ( CZ) 3 C2 ( CZ)
>50.0000 180.0001
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Jul 07 2026 - 07:30:02 PDT
