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:
Modified 10 parameters directly in the Parmed source code:
6 parameters for GB atom radius.
4 parameters for GB screening.
Modified 15 parameters in the 'Amber mdin file' for the sander program:
12 parameters for GB atom parameters.
GB neck scale.
GB offset.
GB probe radius.
Unmodified Parameters:
I was 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
Energy of Generalized Born term has a very significant difference, I am
unable to find out the reason for this much difference. It would be greatly
helpful if you could guide me on figuring this out.
Thank you,
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jan 15 2025 - 23:30:02 PST
