AMBER Archive (2004)

Subject: Re: AMBER: test output of amber8

From: David A. Case (case_at_scripps.edu)
Date: Wed Mar 31 2004 - 19:37:50 CST

On Wed, Mar 31, 2004, Oliver Hucke wrote:
>
> I have just installed amber 8 and run the tests. Most tests pass but for
> some I get the message POSSIBLE FAILURE.
> Mostly antechamber output files, especially charges, seem to be
> different from what is to be expected.
> Below you can find the file sustiva.prepin.dif from the directory
> "tests/antechamber/sustiva" as an example.
> I suppose the differences result from roundoff and are neglectable?

Yes: the sorts of errors you show (included below) are typical for the
antechamber test suite. They are not literally just "roundoff", but
reflect the fact that an AM1 geometry opimization is being done prior to
getting the charges. The optimization stops at slightly different places
on different machines, leading to some variance in charges.

It looks like your charge differences are all less than 0.005 electron, and
this is entirely acceptable. You should pay attention to differences that
are greater than about 0.01 electron.

...thanks for your comments...good luck...dac

> ------------------
> sustiva.prepin.dif:
>
> 11,12c11,12
> < 5 C1 ca M 4 3 2 1.3 86.8 -162.9 -0.049
> < 6 H1 ha E 5 4 3 1.0 120.1 25.5 0.169
> ---
> > 5 C1 ca M 4 3 2 1.3 86.8 -162.9 -0.046
> > 6 H1 ha E 5 4 3 1.0 120.1 25.5 0.167
> 14c14
> < 8 Cl1 cl E 7 5 4 1.7 119.6 -179.8 -0.075
> ---
> > 8 Cl1 cl E 7 5 4 1.7 119.6 -179.8 -0.076
> 17c17
> < 11 C12 ca M 9 7 5 1.3 119.7 0.1 -0.172
> ---
> > 11 C12 ca M 9 7 5 1.3 119.7 0.1 -0.171
> 19,24c19,24
> < 13 C11 ca M 11 9 7 1.3 119.9 -0.5 0.108
> < 14 N1 n M 13 11 9 1.3 121.1 179.9 -0.473
> < 15 H7 hn E 14 13 11 0.9 120.1 3.7 0.356
> < 16 C10 c M 14 13 11 1.3 124.4 -166.5 0.841
> < 17 O2 o E 16 14 13 1.1 123.2 172.5 -0.580
> < 18 O1 os M 16 14 13 1.3 115.7 -5.6 -0.376
> ---
> > 13 C11 ca M 11 9 7 1.3 119.9 -0.5 0.106
> > 14 N1 n M 13 11 9 1.3 121.1 179.9 -0.471
> > 15 H7 hn E 14 13 11 0.9 120.1 3.7 0.355
> > 16 C10 c M 14 13 11 1.3 124.4 -166.5 0.837
> > 17 O2 o E 16 14 13 1.1 123.2 172.5 -0.577
> > 18 O1 os M 16 14 13 1.3 115.7 -5.6 -0.374
> 26,32c26,32
> < 20 C9 c3 3 19 18 16 1.5 105.8 -88.8 0.619
> < 21 F1 f E 20 19 18 1.3 110.0 61.2 -0.228
> < 22 F2 f E 20 19 18 1.3 110.7 -179.3 -0.230
> < 23 F3 f E 20 19 18 1.3 111.5 -58.5 -0.214
> < 24 C4 c1 M 19 18 16 1.4 107.2 154.8 -0.197
> < 25 C5 c1 M 24 19 18 1.1 179.4 175.8 0.013
> < 26 C6 cx M 25 24 19 1.4 179.6 -134.9 -0.078
> ---
> > 20 C9 c3 3 19 18 16 1.5 105.8 -88.8 0.611
> > 21 F1 f E 20 19 18 1.3 110.0 61.2 -0.231
> > 22 F2 f E 20 19 18 1.3 110.7 -179.3 -0.228
> > 23 F3 f E 20 19 18 1.3 111.5 -58.5 -0.216
> > 24 C4 c1 M 19 18 16 1.4 107.2 154.8 -0.190
> > 25 C5 c1 M 24 19 18 1.1 179.4 175.8 0.014
> > 26 C6 cx M 25 24 19 1.4 179.6 -134.9 -0.079
> 34c34
> < 28 C7 cx M 26 25 24 1.5 119.5 -91.7 -0.107
> ---
> > 28 C7 cx M 26 25 24 1.5 119.5 -91.7 -0.106
> 36c36
> < 30 H4 hc E 28 26 25 1.0 117.3 -0.4 0.082
> ---
> > 30 H4 hc E 28 26 25 1.0 117.3 -0.4 0.083
> 

-- 

==================================================================
David A. Case                     |  e-mail:      case_at_scripps.edu
Dept. of Molecular Biology, TPC15 |  fax:          +1-858-784-8896
The Scripps Research Institute    |  phone:        +1-858-784-9768
10550 N. Torrey Pines Rd.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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