I used sander with igb=10 ( to activate pbsa calculation as in manual) with
vacuum trajectory with ions and solvent removed.
&cntrl
imin=5,
gbsa=1,
surften=1,
igb=10,
extdiel=80,
ntb=0,
cut=999,
/
I have pasted one step of the output file , are these values wrong and how
can I use this to calculate the solvent accessible surface area.
NSTEP ENERGY RMS GMAX NAME NUMBER
1 -3.0254E+04 2.5720E+04 1.1428E+06 H15 44
BOND = 525.7356 ANGLE = 1587.0521 DIHED =
2382.5603
VDWAALS = -834.0068 EEL = -6765.5983 EPB =
-8295.6367
1-4 VDW = 668.9895 1-4 EEL = 13074.6001 RESTRAINT =
0.0000
ESURF = 778.0734
ECAVITY = 778.0734 EDISPER = -33375.9444
minimization completed, ENE= -.30254175E+05 RMS= 0.257198E+05
minimizing coord set # 22
Cavity solvation energy 780.7086
Dispersion solvation energy-235747.0585
Here I try to analyze the efffect of certain addtives on the solvation free
energy of my hydrophilic polymer
In this trajectory I have only removed the solvent and ions and I have used
a vacuum topology file similar to the trajectory.
Thanks
Kirtana
On Mon, Apr 9, 2012 at 4:38 PM, David A Case <case.biomaps.rutgers.edu>wrote:
> On Mon, Apr 09, 2012, kirtana S wrote:
>
> > Will this give meaningful results if I use the trajectory obtained from
> the
> > explicit water simulations by removing water and using nobox to obtain my
> > new trajectory.
> > And use a vacuum topology file of the polymer by itself .
> > Can I obtain the solvation free energy using MMPBSA.
>
> The "PBSA" part of mmpbsa will estimate the solvation free energy of each
> snapshot you save, and the "MM" part will average over snapshots. So the
> general answer is "yes" you should be able to use mm-pbsa to get an average
> solvation free energy. You could then do it again with a different ionic
> strength to get some feeling for the effect of ionic strength on solvation
> free energy. To the extent that PB theory "works", these estimates may be
> helpful, (although it is still somewhat unclear to me what one would do
> with
> such numbers once they were computed.)
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 09 2012 - 19:00:03 PDT
