On Thu, Aug 03, 2017, Shilpa Gupta wrote:
>
> I have simulated protein in the presence of water model
> SPCFw and in the output file of the simulation i have got Number of
> triangulated 3-point waters found: 0. When i build the pdb from the
> restart file i have got the coordinates of water molecule so i could not
> understand that in the output file why there are no triangulated 3-point
> waters present. The input is given as the mentioned in the attached pdf
> file. Thanks in advance.
This is expected: SPCFw is a flexible water, and has no bond between the two
H atoms. Hence, in Amber lingo, it is not "triangulated".
Be sure you actually want to use the SFCFw model: it is very rarely used.
The overwheliming majority of biomolecular simulations use a rigid water
model.
....dac
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Received on Thu Aug 03 2017 - 05:30:04 PDT
