AMBER Archive (2004)

Subject: Re: AMBER: MM_PBSA reproduction of literature values and accuracy

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Mon Oct 25 2004 - 12:53:50 CDT

Karl,
I'm not sure I understand how you've done the calculation in terms
of the intial and final states. Are you subtracting out gas phase values? I
don't use mmpbsa scripts myself (just run the programs directly),
so I don't know exactly what yove' done. It seems like the entropy
values are really big though, are those the same units as the other terms?
Are those total entropies, or the difference in entropy due to solvation?
Normally I use mm-pbsa to calculate a difference between two
endpoints such as formation of a complex, all with implicit solvent.
When thinking of the entropy change, what are your endpoints, and what
nmode calculations dod you do for each of them?
without the TSTOT term, your data seems to give reasonable values.
Carlos

===================================================================
Carlos L. Simmerling, Ph.D.
Associate Professor Phone: (631) 632-1336
Center for Structural Biology Fax: (631) 632-1555
Stony Brook University Web: http://comp.chem.sunysb.edu/carlos
Stony Brook, NY 11794-5115 E-mail: carlos.simmerling_at_stonybrook.edu
===================================================================

Karl N. Kirschner wrote:

>Hi all,
> In an attempt to test my understanding of the mm_pbsa procedure I am
>trying to reproduce literature values for the solvation free energies of
>ethanol. An article (J. Phys. Chem. B 102 (1998) 9571) uses AMBER with
>the Cornell et al. force field and HF/6-31G* resp charges, scaled atomic
>radii, and a calibrated screening parameter to find a solvation free
>energy of -3.46 kcal/mol. This is in reasonable agreement with the
>cited experimental value of -4.90 kcal/mol.
>
> I have attempted to reproduce these results using AMBER8 MM_PBSA,
>using the parm94 force field, the same ethanol published charge set
>published, and by running a 1 ns simulation of ethanol in explicit TIP3P
>waters. Below is the results that I found:
>
># MEAN STD
># =======================
>ELE -13.73 0.32
>VDW 0.32 0.23
>INT 4.57 1.55
>GAS -8.84 1.58
>GBSUR 1.42 0.01
>GB -7.33 0.25
>GBSOL -5.92 0.24
>GBELE -21.07 0.28
>GBTOT -14.76 1.58
>TSTRA 11.21 0.00
>TSROT 6.69 0.00
>TSVIB 1.53 0.00
>TSTOT 19.43 0.00
>
>So, my question comes to is this - have I incorrectly calculated
>ethanol's free energy of solvation by incorrectly setting up the mm_pbsa
>calculation up? I have even varied the charge set and have not found a
>difference in the results to the magnitude I need. I have also viewed
>the trajectory using vmd and it appears fine. Below is my input for the
>mm_pbsa:
>
>##################
>@GENERAL
>#
>PREFIX ethanol_water_md
>PATH ./GenerateSnapshots
>#
>COMPLEX 0
>RECEPTOR 1
>LIGAND 0
>#
>COMPT XXX
>RECPT ../ethanol.top
>LIGPT XXX
>#
>GC 1
>AS 0
>DC 0
>#
>MM 1
>GB 1
>PB 0
>MS 1
>#
>NM 1
>#
>##########
>@MAKECRD
>BOX YES
>NTOTAL 1377
>NSTART 50
>NSTOP 1000
>NFREQ 1
>#
>NUMBER_LIG_GROUPS 0
>NUMBER_REC_GROUPS 1
>RSTART 1
>RSTOP 9
>#
>################
>@TRAJECTORY
>TRAJECTORY ../ethanol_water_md.crd
>################
>@MM
>DIELC 1.0
>################
>@GB
>IGB 2
>GBSA 1
>SALTCON 0.00
>EXTDIEL 80.0
>INTDIEL 1.0
>#
>SURFTEN 0.0072
>SURFOFF 0.00
>#
>###############
>@MS
>PROBE 0.0
>###############
>@NM
>DIELC 4
>MAXCYC 10000
>DRMS 0.01
>###############
>
>Any help in my understanding where I might be going wrong, and any
>comments the general sense of the accuracy of mm_pbsa would be
>appreciated.
>
>Cheers,
>Karl
>
>
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