AMBER Archive (2002)

Subject: mm_pbsa-amber7

From: Sue Heavner (sheavner_at_hsc.wvu.edu)
Date: Tue Oct 22 2002 - 14:06:01 CDT

Hi all:
After installing delphi and successfully running the example in
mm_pbsa/Examples/02_MMPBSA_stability I tried to run mm_pbsa for my
polyCG DNA. Specifically I am telling it to do the gas phase, GB, PB,
and nmode calculations. I am using the atmtypenumbers file in the
Examples, amber94_delphi.crg_4 from amber6, and my_parse_delphi.siz from
amber7. I get the following output:
        MEAN STD
ELE -833.91 18.88
VDW -172.29 5.49
INT 943.57 16.53
GAS 62.63 17.43
PBSUR 16.74 0.07
PBCAL 0.00 0.00
PBSOL 16.74 0.07
PBELE -833.91 18.88
PBTOT -45.89 17.38
GBSUR 22.11 0.09
GB -4485.04 7.30
GBSOL -4462.92 7.33
GBELE -5318.94 14.05
GBTOT -4525.55 10.91
TSTRA 15.57 0.00
TSROT 15.19 0.00
TSVIB 191.99 1.15
TSTOT 522.74 1.16
I am doing the calculation on three frames of a 2ns traj just to see if
worked. Does anyone know why the PBCAL term is not being calculated?
The program is not giving any errors. Thank-you, Sue Heavner