AMBER Archive (2009)

Subject: [AMBER] AMBER 10: sleap diff errors?

From: Catein Catherine (askamber23_at_hotmail.com)
Date: Thu Jun 04 2009 - 00:37:35 CDT

Dear Sir/Madam,

 

I noted one Test_failure files after AMBER10 installation. in sleap folder as follows, is it necessary to correct this error. Does it only affect the sleap but not xleap? What should I do to correct this error? Thank you very much!

 

/home/cmche/amber10/test/sleap/pdbent
9c9
< 3403 3431 279 

---
>     1631     1579      279
13,3415c13,1643
<        1 N           13.120    39.003     5.159 N3              1 PROA1       -0.202
<        2 H2          13.466    38.055     5.190 H               1 PROA1        0.312
<        3 H3          13.599    39.698     4.605 H               1 PROA1        0.312
<        4 CD          11.746    39.019     4.650 CT              1 PROA1       -0.012
<        5 HD2         11.672    38.364     3.782 HP              1 PROA1        0.100
<        6 HD3         11.477    40.035     4.362 HP              1 PROA1        0.100
<        7 CG          10.966    38.512     5.856 CT              1 PROA1       -0.121
<        8 HG2         11.199    37.461     6.024 HC              1 PROA1        0.100
<        9 HG3          9.897    38.621     5.670 HC              1 PROA1        0.100
<       10 CB          11.457    39.390     6.893 CT              1 PROA1       -0.115
<       11 HB2         11.231    38.962     7.870 HC              1 PROA1        0.100
<       12 HB3         10.975    40.364     6.804 HC              1 PROA1        0.100
.....

possible FAILURE:  check hpv.off.dif
/home/cmche/amber10/test/sleap/offlib
4,3131c4,3131
<  "N" "N3" 0 1 131072 1 7 -0.202000
<  "H2" "H" 0 1 131072 2 1 0.312000
<  "H3" "H" 0 1 131072 3 1 0.312000
<  "CD" "CT" 0 1 131072 4 6 -0.012000
<  "HD2" "HP" 0 1 131072 5 1 0.100000
<  "HD3" "HP" 0 1 131072 6 1 0.100000

 
 
possible FAILURE:  check source.out.dif
/home/cmche/amber10/test/sleap/source
4,173c4
< logFile leap.log
< #
< # ----- leaprc for loading the parm99 additive force field, no lone pairs
< #       assumes that any unspecified nucleic acids are DNA
< #
< #   load atom type hybridizations
< #
< addAtomTypes {
<     { "H"   "H" "sp3" }
<     { "HO"  "H" "sp3" }
<     { "HS"  "H" "sp3" }
<     { "H1"  "H" "sp3" }
<     { "H2"  "H" "sp3" }
<     { "H3"  "H" "sp3" }
<     { "H4"  "H" "sp3" }

 
 
etc.......
 
 
 
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