Hi,
I am using the recently developed GB99dms force field, a modification of
the a99SBdisp + GBNeck2 implicit solvent model. This force field is
compatible with OpenMM and available at
https://github.com/greener-group/GB99dms. I want to use this force field in
Amber, and as part of this, I am updating all 108 modified parameters in
the older force field.
So far, I have successfully updated the protein force field parameters and
generated the corresponding parameter file (using Parmed too). This update
is reflected in the energy decomposition analysis shown below. However, out
of the 27 GBNeck2 parameters, I was only able to update 25.
https://pubs.rsc.org/en/content/articlelanding/2024/sc/d3sc05230c (page 4,
supplementary data).
GB Parameters:
I have modified 6 parameters for GB atom radius and 4 parameters for GB
screening directly in the Parmed source code.
I have also modified 12 parameters for GB atom parameters, GB neck scale,
GB offset, and GB probe radius in the 'Amber mdin file' for the sander
program
But I am unable to update the *GB neck cutoff* and *GB SA factor*
parameters,
(although their changes are negligible).
Energy Comparison:
After updating the parameters, I calculated the energy for a specific
protein conformation using OpenMM and Amber. The results for the different
energy terms are as follows:
Energy- Term Energy (OpenMM) Energy (Amber)
BOND 804.270819631023 804.2708
ANGLE 307.25486784669033 307.2549
DIHEDRAL -6804.342259361988 -6804.3423
Non-bonded 1928.0139766568032 1927.99
*Generalized Born -5120.42045026855 -5201.0504*
Total Energy -8885.223111155796 -8965.9
The energy of the Generalized Born term (CustomGBForce in OpenMM) has a
very significant difference, I am
unable to find out the reason for this much difference.
I would greatly appreciate your guidance on the following -
- How can I modify the *GB neck cutoff* and *GB SA factor* parameters in
the Amber or ParmEd source code?
- What could be the possible reasons for the significant difference in the
Generalized Born energy term between OpenMM and Amber calculations?
Thank you,
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Received on Tue Jan 21 2025 - 04:30:02 PST
