AMBER Archive (2005)
Subject: Fwd: Re: AMBER: AMBER Test

From: Anthony Cruz (acb15885_at_uprm.edu)
Date: Wed May 11 2005 - 10:49:38 CDT

Previous message: Thomas E. Cheatham, III: "Re: AMBER: Asking how to creat alanine "dipeptide" in amber8"
Next in thread: David A. Case: "Re: Fwd: Re: AMBER: AMBER Test"
Reply: David A. Case: "Re: Fwd: Re: AMBER: AMBER Test"
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After applying the bugfix.all and compile again 1 test dont pass:

How can fix it???
==============================================================
cd pb_pgb; ./Run.pbpgb
diffing mdout.pbpgb.save with mdout.pbpgb
possible FAILURE: check mdout.pbpgb.dif
==============================================================

acruz_at_tccg5:~/amber/amber8/test/pb_pgb> more mdout.pbpgb.dif
66c66
< Etot = -14371.5201 EKtot = 3870.9870 EPtot =
-18242.5071

---
>  Etot   =    -14329.6226  EKtot   =      3870.9870  EPtot      =    
-18200.6096
69c69,70
<  EELEC  =    -24281.4685  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24281.4685  EGB     =         0.0000  RESTRAINT  =        
41.8975
>  EAMBER (non-restraint)  =    -18242.5071
72c73
<  Etot   =    -14371.3557  EKtot   =      3855.1841  EPtot      =    
-18226.5398
---
>  Etot   =    -14329.7248  EKtot   =      3855.1841  EPtot      =    
-18184.9089
75c76,77
<  EELEC  =    -24277.4299  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24277.4299  EGB     =         0.0000  RESTRAINT  =        
41.6310
>  EAMBER (non-restraint)  =    -18226.5398
78c80
<  Etot   =    -14371.0657  EKtot   =      3845.7886  EPtot      =    
-18216.8542
---
>  Etot   =    -14329.6623  EKtot   =      3845.7886  EPtot      =    
-18175.4508
81c83,84
<  EELEC  =    -24274.7240  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24274.7240  EGB     =         0.0000  RESTRAINT  =        
41.4034
>  EAMBER (non-restraint)  =    -18216.8542
84c87
<  Etot   =    -14371.2605  EKtot   =      3843.8455  EPtot      =    
-18215.1060
---
>  Etot   =    -14330.0477  EKtot   =      3843.8455  EPtot      =    
-18173.8933
87c90,91
<  EELEC  =    -24273.3960  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24273.3960  EGB     =         0.0000  RESTRAINT  =        
41.2128
>  EAMBER (non-restraint)  =    -18215.1060
90c94
<  Etot   =    -14371.3474  EKtot   =      3848.9511  EPtot      =    
-18220.2985
---
>  Etot   =    -14330.2871  EKtot   =      3848.9511  EPtot      =    
-18179.2382
93c97,98
<  EELEC  =    -24272.3671  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24272.3671  EGB     =         0.0000  RESTRAINT  =        
41.0603
>  EAMBER (non-restraint)  =    -18220.2985
96c101
<  Etot   =    -14371.4557  EKtot   =      3859.3314  EPtot      =    
-18230.7872
---
>  Etot   =    -14330.5031  EKtot   =      3859.3314  EPtot      =    
-18189.8346
99c104,105
<  EELEC  =    -24271.6192  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24271.6192  EGB     =         0.0000  RESTRAINT  =        
40.9526
>  EAMBER (non-restraint)  =    -18230.7872
102c108
<  Etot   =    -14371.5396  EKtot   =      3872.1405  EPtot      =    
-18243.6801
---
>  Etot   =    -14330.6588  EKtot   =      3872.1405  EPtot      =    
-18202.7993
105c111,112
<  EELEC  =    -24270.6614  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24270.6614  EGB     =         0.0000  RESTRAINT  =        
40.8808
>  EAMBER (non-restraint)  =    -18243.6801
108c115
<  Etot   =    -14371.4401  EKtot   =      3884.4149  EPtot      =    
-18255.8550
---
>  Etot   =    -14330.6005  EKtot   =      3884.4149  EPtot      =    
-18215.0154
111c118,119
<  EELEC  =    -24269.1041  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24269.1041  EGB     =         0.0000  RESTRAINT  =        
40.8396
>  EAMBER (non-restraint)  =    -18255.8550
114c122
<  Etot   =    -14371.3442  EKtot   =      3893.7656  EPtot      =    
-18265.1098
---
>  Etot   =    -14330.5209  EKtot   =      3893.7656  EPtot      =    
-18224.2865
117c125,126
<  EELEC  =    -24267.0114  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24267.0114  EGB     =         0.0000  RESTRAINT  =        
40.8233
>  EAMBER (non-restraint)  =    -18265.1098
120c129
<  Etot   =    -14371.0865  EKtot   =      3898.7752  EPtot      =    
-18269.8617
---
>  Etot   =    -14330.2612  EKtot   =      3898.7752  EPtot      =    
-18229.0364
123c132,133
<  EELEC  =    -24264.0719  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24264.0719  EGB     =         0.0000  RESTRAINT  =        
40.8253
>  EAMBER (non-restraint)  =    -18269.8617
127c137
<  Etot   =    -14371.3416  EKtot   =      3867.3184  EPtot      =    
-18238.6599
---
>  Etot   =    -14330.1889  EKtot   =      3867.3184  EPtot      =    
-18197.5073
130c140,141
<  EELEC  =    -24272.1854  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =    -24272.1854  EGB     =         0.0000  RESTRAINT  =        
41.1527
>  EAMBER (non-restraint)  =    -18238.6599
134c145
<  Etot   =         0.1555  EKtot   =        18.9232  EPtot      =        
18.9344
---
>  Etot   =         0.3805  EKtot   =        18.9232  EPtot      =        
19.1072
137c148,149
<  EELEC  =         4.7577  EGB     =         0.0000  RESTRAINT  =         
0.0000
---
>  EELEC  =         4.7577  EGB     =         0.0000  RESTRAINT  =         
0.3586
>  EAMBER (non-restraint)  =        18.7485
----------  Forwarded Message  ----------
Subject: Re: AMBER: AMBER Test
Date: Tuesday 26 April 2005 10:12 am
From: David Case <case_at_scripps.edu>
To: amber_at_scripps.edu
On Tue, Apr 26, 2005, Anthony Cruz wrote:
> cd nonper; ./Run.cap
> diffing mdout.cap.save with mdout.cap
> possible FAILURE:  check mdout.cap.dif
>
>
> acruz_at_tccg5:~/amber/amber8/test/nonper> more mdout.cap.dif
> 76c76
> <  Etot   =     -3409.9453  EKtot   =      2056.0343  EPtot      =
> -5465.9796
> ---
>
> >  Etot   =     -3404.4787  EKtot   =      2056.0343  EPtot      =
>
> -5460.5130
Please see bugfix.43.
> cd pb_pgb; ./Run.pbpgb
> diffing mdout.pbpgb.save with mdout.pbpgb
> possible FAILURE:  check mdout.pbpgb.dif
>
>
> acruz_at_tccg5:~/amber/amber8/test/pb_pgb> more mdout.pbpgb.dif
> 66c66
> <  Etot   =    -14371.5201  EKtot   =      3870.9870  EPtot      =
> -18242.5071
> ---
>
> >  Etot   =    -14329.6226  EKtot   =      3870.9870  EPtot      =
>
> -18200.6096
This looks like the same problem, but I don't see a bugfix for it.  The error
is innocuous.
...dac
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Previous message: Thomas E. Cheatham, III: "Re: AMBER: Asking how to creat alanine "dipeptide" in amber8"
Next in thread: David A. Case: "Re: Fwd: Re: AMBER: AMBER Test"
Reply: David A. Case: "Re: Fwd: Re: AMBER: AMBER Test"
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AMBER Archive (2005)Subject: Fwd: Re: AMBER: AMBER Test

AMBER Archive (2005)
Subject: Fwd: Re: AMBER: AMBER Test