AMBER: adenine test for LMOD in amber8

From: Giulio Rastelli <rastelli.giulio.unimo.it>
Date: Thu, 16 Jun 2005 11:57:16 +0200

Dear Amber users and Prof. Kolossvary,
I have compiled sander (amber8) with the -lmod
flag on a SGI fuel (./configure -lmod sgi_mips); compilation is fine and
the test.lmod completes successfully.
However, the adenine.lmod.out significantly differs
from the adenine.lmod.save file provided with amber8.
It seems that the .save file is broken, with this error
message:
ERROR in load_lbfgs(): YS=0.
Anyhow, the numbers before the error message are different:


--5,17c5,78
< 2 / 2 E = 0.362285 ( 0.099) Rg = 1.216 rmsd= 0.708 p=1.0000
< 2 /20 E = 1.73958 ( 0.095) Rg = 1.221 rmsd= 0.307 p=
0.4537
< 3 /20 E = 5.27472 ( 0.079) Rg = 1.339 rmsd= 1.172 p=
0.0430
< 3 / 4 E = 1.35929 ( 0.096) Rg = 1.045 rmsd= 1.798 p=
0.5846
< 9 / 2 E = 0.87711 ( 0.077) Rg = 1.238 rmsd= 0.795 p=
0.8063
< 9 / 2 E = 1.17001 ( 0.096) Rg = 1.274 rmsd= 1.052 p=
0.6633
<
---------------------------------------------------------------------------
< 2 E = 1.35929 ( 0.096) Rg = 1.045
< 4 / 5 E = 1.70444 ( 0.090) Rg = 1.299 rmsd= 1.314 p=
0.7945
< 4 / 3 E = 2.7002 ( 0.084) Rg = 1.169 rmsd= 0.807 p=
0.4090
< 6 / 5 E = 3.1133 ( 0.099) Rg = 1.057 rmsd= 0.724 p=
0.3106
< 6 / 8 E = 2.29528 ( 0.080) Rg = 0.994 rmsd= 0.928 p=
0.5358
< ERROR in load_lbfgs(): YS=0. 
---
 >   2  / 2  E =     0.457557 ( 0.083)  Rg =    1.222  rmsd=  0.734  p= 
1.0000
 >   2  /20  E =      1.63551 ( 0.084)  Rg =    1.217  rmsd=  0.355  p= 
0.4863
 >   3  / 2  E =      3.53393 ( 0.099)  Rg =    1.369  rmsd=  1.100  p= 
0.1372
 >   3  / 9  E =     -4.05462 ( 0.304)  Rg =    1.024  rmsd=  2.459  p= 
1.0000
 >   9  / 2  E =     0.842456 ( 0.088)  Rg =    1.236  rmsd=  0.782  p= 
0.8251
 >   9  / 2  E =       1.2017 ( 0.086)  Rg =    1.269  rmsd=  1.052  p= 
0.6494
 > 
---------------------------------------------------------------------------
 >      2    E =     -4.05462 ( 0.304)  Rg =    1.024
 >   4  / 2  E =     -6.37122 ( 0.095)  Rg =    1.034  rmsd=  0.453  p= 
1.0000
 >   4  /17  E =     -7.37857 ( 0.093)  Rg =    1.074  rmsd=  0.968  p= 
1.0000
 >   6  / 2  E =     -6.46066 ( 0.098)  Rg =    1.035  rmsd=  0.516  p= 
1.0000
 >   6  / 2  E =     -6.43774 ( 0.084)  Rg =    1.030  rmsd=  0.470  p= 
1.0000
 >   7  / 3  E =       -6.476 ( 0.098)  Rg =    1.036  rmsd=  0.542  p= 
1.0000
 >   7  / 2  E =      4.62435 ( 0.093)  Rg =    1.095  rmsd=  1.382  p= 
0.0031
Any advise on how to procede?
Thanks very much in advance
Prof. Giulio Rastelli
Dipartimento di Scienze Farmaceutiche
Facolta' di Bioscienze e Biotecnologie
Universita' di Modena e Reggio Emilia
Via Campi 183
41100 Modena - ITALY
-------------------------------------
tel 0039-059-2055145
fax 0039-059-2055131
-------------------------------------
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Received on Thu Jun 16 2005 - 11:53:00 PDT
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