Dear Amber users,
I have corrected my input and script file according to earlier interaction
with mailing list archive and proceeded to calculate SASA but end with very
High ESURF for protein with 123 amino acids. Kindly help me in this regard.
ESURF=surften * SASA, this is true?
input file
calculate solvent accessible surface area
&cntrl
imin=5,
ntb=0,
igb=2,
cut=15.0,
gbsa=2,
surften=1,
&end
Here is the script file
sander -O -i SASA.in -o SASA.out -p TY.top -c TY.crd -y TY.mdcrd
Removed water from mdcrd file using ptraj and also accordingly edited top
and crd file.
Here is the result
4. RESULTS
--------------------------------------------------------------------------------
POST-PROCESSING OF TRAJECTORY ENERGIES
trajectory generated by ptraj
minimizing coord set # 1
NSTEP ENERGY RMS GMAX NAME NUMBER
1 4.3838E+03 1.7560E+01 1.0670E+02 CD 953
BOND = 388.3529 ANGLE = 1053.5701 DIHED =
1449.9245
VDWAALS = -951.5401 EEL = -9155.0578 EGB =
-1398.5951
1-4 VDW = 489.3395 1-4 EEL = 4165.6309 RESTRAINT =
0.0000
ESURF = 8342.2177
Maximum number of minimization cycles reached.
FINAL RESULTS
NSTEP ENERGY RMS GMAX NAME NUMBER
1 4.3838E+03 1.7560E+01 1.0670E+02 CD 953
BOND = 388.3529 ANGLE = 1053.5701 DIHED =
1449.9245
VDWAALS = -951.5401 EEL = -9155.0578 EGB =
-1398.5951
1-4 VDW = 489.3395 1-4 EEL = 4165.6309 RESTRAINT =
0.0000
ESURF = 8342.2177
like this results were obtained for all the frames...
Thanks in advance,
siddharth Rastogi
--
Siddharth Rastogi
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Received on Fri Dec 05 2008 - 15:00:19 PST
