AMBER Archive (2008)

Subject: AMBER: Solvent Accesible Surface Area (SASA) - Confused

From: Deepangi Pandit (dpandit_at_brandeis.edu)
Date: Fri Aug 29 2008 - 13:45:19 CDT

Hi All:
       After referring messages from AMBER archive, I tried to calculate SASA over the entire trajectory using following command and input file. However, I am unable to find SASA in the output file. I am not sure what is missing. Your help is appreciated.

Thank you.
Deepa

command:
sander -O -i msr_SASA.in -p dry_apr7.prmtop -c dry_apr7.inpcrd -x pro_reimg_strip.binpos -o msr_SASA.out

input:

&cntrl
 ntb=0
 igb=1,
 cut=999.,
 rgbmax=999
 imin = 5,
 gbsa=2,
 surften=1
/

selected output:

--------------------------------------------------------------------------------
   3. ATOMIC COORDINATES AND VELOCITIES
--------------------------------------------------------------------------------

 begin time read from input coords = 0.000 ps

 Number of triangulated 3-point waters found: 0

--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 POST-PROCESSING OF TRAJECTORY ENERGIES
 Trajectory file ended

--------------------------------------------------------------------------------
   5. TIMINGS
--------------------------------------------------------------------------------

| Read coords time 0.06 (27.37% of Total)
| Fast Water setup 0.00 ( 0.04% of Total)
| Other 0.15 (72.59% of Total)
                                                                                                                                           123,1 89%

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