AMBER Archive (2005)

Subject: AMBER: mmpbsa test problem

From: Suxin Zheng (sxzheng_at_u.washington.edu)
Date: Fri Jul 22 2005 - 20:41:11 CDT

Dear amber,

When I test the mmpbsa module in Amber8/src/mm_pbsa/Examples/
03_MMPBSA_Binding, it gives out:

=>> Calculating energy / entropy contributions
     Calc contrib for ../01_GenerateSnapshots/ras_raf_II_wt_com.crd.1
         Calc MM/GB/SAS
1525-090 The NAMELIST READ statement cannot be completed because an
incorrect character was encountered in a NAMELIST group name or item
name. The program will recover by discontinuing further processing
of the READ statement.
STOP 0

After I search the list, I use export XLFRTEOPTS=namelist=old to fix
up this NAMELIST problem.

But the results have something different from the
ras_raf_II_wt_statistics.out.save, especially in the PB term.
The ras_raf_II_wt_statistics.out.save as:

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -1287.43 18.06
VDW -61.29 1.40
INT 0.00 0.00
GAS -1348.73 18.01
PBSUR -7.20 0.11
PBCAL 1291.06 14.03
PBSOL 1283.86 14.11
PBELE 3.63 15.78
PBTOT -64.87 14.88
GBSUR -10.37 0.15
GB 1307.66 14.77
GBSOL 1297.29 14.91
GBELE 20.23 3.57
GBTOT -51.43 3.76

While the result I get as:

# DELTA
# -----------------------
# MEAN STD
# =======================
ELE -1287.43 18.06
VDW -61.29 1.40
INT 0.00 0.00
GAS -1348.73 18.01
PBSUR -7.02 0.11
PBCAL 1289.71 14.17
PBSOL 1282.69 14.24
PBELE 2.27 15.99
PBTOT -66.04 15.10
GBSUR -10.11 0.16
GB 1307.66 14.77
GBSOL 1297.55 14.92
GBELE 20.23 3.57
GBTOT -51.18 3.77

Have you met this problem. What cause the difference and how to fix
it. I run amber8 on Mac G5.

Suxin

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