Dear Amber community,
I'm trying to run the TI simulation of mutating an amino acid to another
one and also vanishing a sodium ion simultaneously. I was wondering if
there's any possibility that I can extract the energy change contribution
of vanishing a sodium ion from the total MABR energy analysis given by
AMBER.
I tried cpptraj energy command to extract the energy of vanishing a sodium
ion. But it will only give me the energy for each frame of the same state
without the ensemble average energy for other states in MBAR energy
analysis, as in the example below.
*The result from cpptraj energy:*
#Frame na[bond] na[angle] na[dih] na[vdw14] na[elec14]
na[vdw] na[elec] na[kinetic] na[total]
1 0.0000 0.0000 0.0000 0.0000 0.0000
-0.0038 64.1610 0.6023 64.7594
2 0.0000 0.0000 0.0000 0.0000 0.0000
-0.0077 72.2929 2.9868 75.2721
3 0.0000 0.0000 0.0000 0.0000 0.0000
-0.0132 79.3160 2.5614 81.8642
*The result from TI simulation:*
MBAR Energy analysis:
Energy at 0.0100 = -206640.770813
Energy at 0.0435 = -206614.923806
Energy at 0.0870 = -206587.388911
Energy at 0.1304 = -206564.258639
......
Thank you so much for reading this email.
Best,
Fanyu
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Aug 01 2023 - 04:00:02 PDT
