Dear Amber users,
I am currently trying to change 1-4 Lennard-Jones parameters of the
GLYCAM06 ff. My first approach was identifying 1-4 pairs and changing
the LJ interaction between each of these pairs separately using the
changeLJPair command in ParmEd. This gives correct results but only
works well up to certain numbers of glucose units in my system: Using
this procedure, the parameter file size seems to increase quadratically
with the number of glucose units. Therefore, 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. 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.
Thank you very much in advance and best regards,
Richard
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Received on Wed May 24 2023 - 02:30:02 PDT
