Thanks Hai,
That looks perfect, I will try it. Another question I had reading the
manual was whether the angle between two planes might be calculated
during dynamics as some sort of 0-weighted NMR restraint:
" rstwt(1)→rstwt(4) New as of Amber 10 (sander only), users may now
define a single restraint that is a function of multiple distance
restraints, called a "generalized distance coordinate" restraint. ... If
eight atoms are given in iat(1)..iat(8) and all weights are zero, the
restraint is a plane-plane angle restraint."
I'm not sure what this means, but if there's a way for me to get some
meaningful number that reflects the base/base angle when running sander
without applying an actual restraint, this would be even better than
having to run cpptraj.
Bill
On 5/1/16 8:46 PM, Hai Nguyen wrote:
> Bill,
>
> maybe this is what you need? http://archive.ambermd.org/201601/0182.html
>
> Hai
>
> On Sun, May 1, 2016 at 11:00 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
>> I'd like to calculate the angle between pairs of bases. Is this possible
>> in cpptraj?
>>
>> Something logically like
>>
>> angle ( plane (atomspec), plane(atomspec) )
>>
>> Thanks,
>>
>> Bill
>>
>>
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Received on Sun May 01 2016 - 21:00:07 PDT
