AMBER Archive (2008)

Subject: AMBER: High ESURF

From: Siddharth Rastogi (siddharthrastogi08_at_gmail.com)
Date: Mon Nov 17 2008 - 02:07:57 CST

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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