AMBER: antechamber error in test / differences in prmtop files

From: Carsten Detering <detering.u.washington.edu>
Date: Thu, 05 Feb 2004 12:07:07 -0800

Hi again,

I think I got mopac running now, thanks to all who replied; DAvid's
response was it eventually that solved the problem (thanks again). I
copied the content of the /mopac7/runmopac script into the mopac script
mopac.sh in $AMBERHOME/exe and edited it a little. Mopac runs now, but I
still have several error messages when running the test:

Differences in the prmtop files
15,17c15,17
< -2.16845370E+00 2.60578890E+00 -2.07734220E+00 2.46001050E+00
-2.49645510E+00
< 2.42356590E+00 -2.04089760E+00 2.42356590E+00 -2.64223350E+00
2.36889900E+00
< 3.09779100E-01 -4.66490880E+00 3.48045930E+00 
---
  >   3.68090460E+00  3.00667950E+00 -8.36403570E+00  3.64446000E+00
-1.67645160E+00
  >   2.38712130E+00 -2.04089760E+00  2.29600980E+00 -2.89734570E+00
2.18667600E+00
  >  -1.45778400E+00 -4.11823980E+00  3.31645860E+00
Although there might be differences in the values on different machines, 
I consider these rather dramatic. Could anyone please comment on this?
The difference in the tp.prepin files are less dramatic, but some of the 
values have opposite signs, which worries me a little:
10,15c10,15
    CG    ca     ...  -0.119
    H32   ha           0.143
    CD1   ca          -0.114
    H29   ha           0.135
    CE1   ca          -0.137
    H30   ha           0.133
----
    CG    ca     ...   0.202
    H32   ha           0.165
    CD1   ca          -0.459
    H29   ha           0.200
    CE1   ca          -0.092
    H30   ha           0.131
17,22c17,22
    H31   ha     ...   0.133
    C6    ca          -0.145
    HE2   ha           0.130
    CD2   ca           0.017
    S15   sh          -0.256
    H19   hs           0.191
----
    H31   ha     ...   0.126
    C6    ca          -0.159
    HE2   ha           0.120
    CD2   ca          -0.080
    S15   sh          -0.226
    H19   hs           0.182
The test concludes with an error:
.../../../exe/sander -O -i min.in -c prmcrd
   Must have more residues than processors!
[1] MPI Abort by user Aborting program !
[1] Aborting program!
[0] MPI Abort by user Aborting program !
[0] Aborting program!
    Program error
make: *** [test.antechamber] Error 1
I think this error is not important and only occurs because I am running 
amber in parallel?
I am running Amber7 on a dual Xeon machine with Redhat 8.0.
Thanks a lot for helpful comments again,
Carsten
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Received on Thu Feb 05 2004 - 20:53:00 PST
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