Dear AMBER community,
What numbers in the output of MMPSA correspond to?
Does "TOTAL" correspond to deltaG as Gibbs free energy? Or "TOTAL" is
deltaH? If yes, then delta means change (or difference) between two states
(frames). Is this correct?
But change between which frames does it calculate if I apply this script to
a trajectory with 100 frames?
Thank you in advance,
Farkhad
After I apply this script to a single-stranded RNA molecule, it gives me
such output:
GENERALIZED BORN:
Complex:
Energy Component Average Std. Dev. Std. Err. of
Mean
-------------------------------------------------------------------------------
BOND 194.5360 10.3837
7.3423
ANGLE 475.5029 13.8450
9.7899
DIHED 1182.5211 16.2931
11.5209
VDWAALS -273.3005 17.7337
12.5396
EEL -572.9388 1.8384
1.2999
1-4 VDW 253.8736 3.1939
2.2584
1-4 EEL -1978.1188 1.2671
0.8960
EGB -602.5792 9.8895
6.9929
ESURF 44.9712 0.4389
0.3103
G gas -717.9245 64.5548
45.6471
G solv -557.6079 9.4506
6.6826
TOTAL -1275.5325 55.1042
38.9645
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Jul 14 2021 - 17:00:02 PDT
