Dear Dave,
I am sorry for the confusion. Yes, I am saying that it seems to me that
the scnb values don't matter. I calculated for each carbohydrate atom
type combination the ratio of the old 1-4 epsilon (o) and new 1-4
epsilon (n) parameters. Then I modified the GLYCAM06j.dat and
GLYCAM06EPb.dat files by searching for these pairs and substituting
SCNB=1.0 for the calculated ratios SCNB=o/n. Later, I carried out the
test with values of SCNB=n/o. A couple example lines are shown below.
"correct" scaling:
H2-Cg-Cg-Cg 6 0.90 0.00 3. SCEE=1.0
SCNB=.939774 2-Dimethylbutanol Hs=0 charge KNK
Ho-Oh-Cg-H1 1 0.18 0.00 3. SCEE=1.0
SCNB=1.938487 Methanol Hs=0 charge KNK
"inverse" scaling:
H2-Cg-Cg-Cg 6 0.90 0.00 3. SCEE=1.0
SCNB=1.064085 2-Dimethylbutanol Hs=0 charge KNK
Ho-Oh-Cg-H1 1 0.18 0.00 3. SCEE=1.0
SCNB=.515866 Methanol Hs=0 charge KNK
As said before, both of these parameters give similar results.
Thank you again and best regards,
Richard
On 5/24/23 13:55, David A Case wrote:
> 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 - 05:30:02 PDT
