Hi Markus,
2016-08-25 12:43 GMT+02:00 Markus Kaukonen <markus.kaukonen.iki.fi>:
> Dear All,
> I try to calculate the solvation energy of ethanol in water using MMPBSA.py
> to do the GBSA and PBSA calculation.
>
> QUESTION1: How do I set the dielectic constant for GBSA, could not find
> parameter for that in the gb section in the manual?
>
This thread might help answer your question.
http://archive.ambermd.org/201307/0139.html
>
> My command was
> MMPBSA.py -O -i mmpbsa.in -o FINAL_RESULTS_MMPBSA.dat -sp
> eth_solvated.prmtop -cp eth.prmtop -y prod1.mdcrd
>
> In the output file (FINAL_RESULTS_MMPBSA.dat) one has
> for the generalised born:
>
> GENERALIZED BORN:
>
> Complex:
> Energy Component Average Std. Dev. Std. Err. of
> Mean
> ------------------------------------------------------------
> -------------------
> BOND 2.6689 1.5477
> 0.0979
> ANGLE 3.5010 1.4781
> 0.0935
> DIHED 1.4535 0.4764
> 0.0301
> EEL 8.8759 1.0681
> 0.0676
> 1-4 VDW 0.2890 0.2154
> 0.0136
> 1-4 EEL -36.7120 1.1293
> 0.0714
> EGB -9.9038 0.6543
> 0.0414
> ESURF 1.3883 0.0028
> 0.0002
>
> G gas -19.9237 2.1129
> 0.1336
> G solv -8.5156 0.6537
> 0.0413
>
> TOTAL -28.4393 2.0001
> 0.1265
>
> ------------------------------------------------------------
> -------------------
> ------------------------------------------------------------
> -------------------
> Using Quasi-harmonic Entropy Approximation: FREE ENERGY (G) = -50.7898
> ------------------------------------------------------------
> -------------------
> ------------------------------------------------------------
> -------------------
>
> QUESTION2: Which value is the solvation energy?
>
EGB = the electrostatic contribution to the solvation free energy
calculated
by
GB.
ESURF = Non-polar solvation energy
> The input file:
> Input file for running PB and GB
> &general
> endframe=999999, verbose=1,
> entropy=1,
> /
> &gb
> igb=2, saltcon=0.100
> /
> &pb
> istrng=0.100,
> /
>
>
> Terveisin, Markus
>
>
> --
> --www=http://www.iki.fi/markus.kaukonen
> --Markus.Kaukonen.iki.fi
> --office: www.helsinki.fi/kemia/svenskakemen/index_eng.html
> --home: Viinirinne 3 F 12, 02630 Espoo, FIN
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>
Regards,
--
*Bilal Nizami*
School of Health Sciences
University of KwaZulu-Natal
Durban
4000
South Africa
Linkedin: za.linkedin.com/pub/bilal-nizami/49/673/790/
Email: 214573074.stu.ukzn.ac.za
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Received on Thu Aug 25 2016 - 04:00:03 PDT
