Dear Amber users,
I am looking for assistance to develop understanding how the charge
constraints work in constructing the forcefield parameter process in
fragment approach. In this regard, I constructed the force field parameters
for a PEG (CH3-[O-CH2-CH2]-OH). I performed two steps with charge
constraints in the fragment approach.
Step1: Charge constraint 1 (Project: P10258)
MOLECULE1-INTRA-MCC2 = 0.0 | 1 2 3 4 | 12 13 | Remove
Questions: What is the purpose of this charge constraint? and what does 0.0
charge value indicate and what exactly this charge constraint do to
molecule?
After completing this job, I extracted the charge values on these terminal
groups i.e. CH3 and OH and calculated the charge as follows. Please note
that the charge values on both terminal are absolute values.
Charge = total charge on CH3 + total charge on OH /2 = 0.1725 + 0.2177 /2
Charge = 0.195
Step2: Charge constraint 2 (Project: P10259 )
MOLECULE1-INTRA-MCC2 = 0.195 | 1 2 3 4 | R
MOLECULE1-INTRA-MCC2 = -0.195 | 12 13 | R
Questions: What is the role of these constraints? And what 0.195 charge
indicates? Is it total molecule charge? or on the terminal groups?
I have found total charges of individual terminal groups i.e. 0.1725 on CH3
and -0.2177 on OH, while I have used 0.195 value in the step2. How I can
explain this difference in charge? However the charge values are close to
the terminal charges. I am not sure if this is right way to calculate
charges though.
Step2 Repeat: (Project: P10260)
MOLECULE1-INTRA-MCC2 = 0.26 | 1 2 3 4 | R
MOLECULE1-INTRA-MCC2 = -0.26 | 12 13 | R
I this case, I have used the total charge values on terminal groups as it
is.
Charge = total charge on CH3 + total charge on OH /2 = 0.1725 +(- 0.2177) /2
Charge = 0.026
Here I have large difference between charge values of terminal groups and
the value I have used in the charge constraint. This charge value is close
to zero though. How I would explain the role of this difference between
charge values of terminal groups and the charge I used in the constraint.
Finally what is the role of this charge and what exactly this whole step do?
I will be very thankful for the response.
Regards,
Iqbal
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Received on Tue Apr 18 2017 - 10:30:03 PDT
