Hi Amber experts,
I have calculated the PB energies for the binding process between DNA and Netropsin. However, I am getting some curious results that I'd like to understand more and I'd like to hear if any of you have ideas?
I calculated these using PBSA stand-alone (see numbers below). Radii were MBONDI, the remaining details are in the PBSA input options below.
1) The results below are calculated with and without salt concentration. However, the results are very close to each other. I have compared the results with other codes (e.g. APBS) and they get values diverging 8-10 kcal/mol due to the salt effect.
2) I have calculated the results using different grid resolutions (focusing was turned off), yet the results don't really display what I expected in terms of convergence behavior, but instead just fluctuate around the same range of values. Is this the expected behavior for PBSA?
Any insight would be really helpful.
Best regards,
Jesper
Salt concentration = 100mM (istrng=100.000000)
GridRes dEPB
.15 1202.3177
.20 1201.9713
.25 1201.9845
.30 1202.5554
.35 1202.2611
.40 1202.0522
.45 1202.2218
.50 1201.9514
.55 1202.4602
.60 1201.7396
.65 1200.5449
.70 1200.9878
.75 1201.1727
.80 1200.8361
.85 1199.6109
.90 1201.1486
.95 1203.6329
1.0 1202.2278
Salt concentration = 0 mM
GridRes dEPB
.15 1201.9931
.20 1200.3285
.25 1200.1105
.30 1200.4338
.35 1200.0356
.40 1200.5173
.45 1201.1034
.50 1201.0788
.55 1201.0346
.60 1200.3855
.65 1199.6695
.70 1200.2409
.75 1201.1009
.80 1200.4463
.85 1199.1350
.90 1201.1621
.95 1203.6926
1.0 1202.1964
PBSA input file:
PBSA input
&cntrl
imin=0,
ntx=1,
ipb=1,
inp=1,
/
&pb
epsin=1.000000,
epsout=80.000000,
smoothopt=0,
istrng=100.000000,
pbtemp=300,
radiopt=0,
dprob=1.4,
iprob=2.00,
arcres=0.0625,
npopt=0,
solvopt=1,
accept=0.001,
maxitn=10000,
fillratio=2,
space=1.0,
nbuffer=0,
nfocus=1,
fscale=8,
npbgrid=1,
bcopt=5,
eneopt=2,
frcopt=0,
scalec=0,
sasopt=0,
saopt=0,
cutfd=5,
cutnb=0,
nsnba=1,
phiout=0,
phiform=1,
npbverb=1,
sprob=1.4,
rhow_effect=1.000,
use_sav=0,
cavity_surften=0.005420
cavity_offset=-1.008000,
maxsph=400
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jun 16 2013 - 23:00:03 PDT
