On Wed, May 24, 2023, Richard Kullmann via AMBER wrote:
>
>I am currently trying to change 1-4 Lennard-Jones parameters of the
>GLYCAM06 ff.
>I tried to just scale the scnb parameters in the force field files. This
>works in that I can see the changes in ParmEd, but, looking at the
>dihedrals, it seems that the alpha-(1-4) linkages of my polymer are
>less flexible now. I only retain the major maximum and lose the second
>peak. The same goes for the glucose pucker conformations. Here the number
>of unlikely conformations is reduced by a factor of 3.
You should probably ask these questions at the Glycam web site -- I'm not
sure that things that get posted here will come to their attention. I
remember that having scnb=1 (i.e. no scaling) was a key feature in the
development of the force field. Indeed, it led to the changes that allowed
different values for scnb for different atom pairs.
>Now, in order to double check the correct implementation of scnb scaling
>factors, I just tried to use inverse values. Surprisingly, the results now
>look very similar to what I got with my first choice of scnb values. So, I
>would like to know how 1-4 scaling is implemented in GLYCAM, and am looking
>for reasons for this strange behavior I'm seeing.
A more explicit example might help here, as I'm lost in your wording. You
seem to be saying that using inverse values of scnb led to the same results
as your "first choice". Are you saying that the value of scnb doesn't
matter? Can you provide an example of what scnb values you used, and
exactly how to went about modifying them?
....dac
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Received on Wed May 24 2023 - 05:00:04 PDT
