AMBER Archive (2005)Subject: AMBER: adenine test for LMOD in amber8
From: Giulio Rastelli (rastelli.giulio_at_unimo.it)
Date: Thu Jun 16 2005 - 04:57:16 CDT
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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