Hello all,
I was looking for PB parameter setting (in MMPBSA.py) which allow for more
realistic
response to "istrng" parameter then the model with default setting (e.g.
eneopt = 2, bcopt = 5)
provides. For me is also important, that this model is proper one for
analyses of charged systems
(this requirement is probably correlated with that first one ).
I found one interesting contribution related to my topic:
http://archive.ambermd.org/201102/0114.html
where is for example suggested to switch to: eneopt = 1 bcopt = 6
I did some small tests with relatively small charged molecule (spherical
hyperbranched polymer, charge +32) and
the sensitivity to istrng parameter was really improved.
I also tried NONlinear PB using (eneopt = 1, bcopt = 6) - below are
results of my small test including GB.
I would like just to ask for any other recommendations/warnings etc.
For example it seems that switching to ( eneopt = 1, bcopt = 6 ) is at
least in linearised PB step
in a good directon (regarding my systems/requirements). On the other hand
there might be even more suitable
settings and what is important change of some parameters from default
might implicate also adjusting of another
parameters. For example in above contribution is written that the default
linearised PB model has
very good grid-independence behavior in solvation energies. So maybe for
example grid spacing is here set
on value which might be almost insufficient for another setting ...
Of course it is also question if one find some reasonable setting for
linearized PB if the same is ideal for
nonlinearized version, which is probably the best choice for charged
systems but also considerably slower
than linearized one ...
I would be grateful for any even general advices/recommendations !
Thanks in advance
Best wishes
Marek
#My tests with positively charged PPI dendrimer. Here the response to
istrng/saltcon parameter is tested
(done all due to the overlook with "use_sander=1" which anyway should not
have big impact (comparing to default) on results (except time
requirements :)) )).
#GB (DEFAULT)
saltcon=0.0 TOTAL -307.6173
saltcon=0.01 TOTAL -349.1688
saltcon=0.1 TOTAL -395.5508
saltcon=0.15 TOTAL -404.0373
saltcon=0.2 TOTAL -409.7319
#linear PB (DEFAULT e.g. eneopt = 2 bcopt = 5 )
istrng=0.0 TOTAL -447.0705
istrng=0.01 TOTAL -446.9819
istrng=0.1 TOTAL -447.5793
istrng=0.15 TOTAL -447.3987
istrng=0.2 TOTAL -447.9070
#linear PB eneopt = 1 bcopt = 6
istrng=0.0 TOTAL -525.0434
istrng=0.01 TOTAL -568.6653
istrng=0.1 TOTAL -605.1151
istrng=0.15 TOTAL -607.3129
istrng=0.2 TOTAL -608.5152
#NON linear PB eneopt = 1 bcopt = 6
istrng=0.01 TOTAL -669.5667
istrng=0.1 TOTAL -675.4274
istrng=0.2 TOTAL -673.7660
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Received on Tue Oct 04 2011 - 18:30:03 PDT
