On Thu, May 15, 2014, Duggan, Brendan wrote:
>
> # 1 PAL H18 1 PAL C18 1 PAL C17 1 PAL H17 160 170 190 200
> &rst
> iat = 53, 3, 4, 34,
> r1 = 160.0, r2 = 170.0, r3 = 190.0, r4 = 200.0,
> rk2 = 2.0, rk3 = 2.0,
> &end
>
> In the starting co-ordinates the value of this torsion as measured by
> cpptraj was -179.8360o . After a one step MD run the sander output
> reports the restraint as violated.
>
> ------------------------------------------------------------------------------
> First atom Last atom curr. value target deviation penalty
> ------------------------------------------------------------------------------
> C18 PLM 1 -- C17 PLM 1: 315.813 190.000 125.813 1.472 t
> Total torsion penalty: 1.472
So, sander thinks the torsion is way different from what cpptraj thinks it is.
I would suggest loading the initial structure into a visualization program
and see what the angle *really* is. Then you'll know which program is getting
it wrong, and can work on debugging from there, e.g. checking that the
atom numbers are really 53,3,4 and 34, etc. (if sander seems wrong), or
double-checking your atom expressions (if cpptraj seems wrong).
...dac
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Received on Thu May 15 2014 - 12:30:04 PDT
