AMBER Archive (2007)

Subject: Re: AMBER: junk in `Noshake mask` output section

From: David A. Case (case_at_scripps.edu)
Date: Wed May 30 2007 - 16:47:51 CDT

On Wed, May 30, 2007, Ben Sattelle wrote:
>
> the principle difference between 'normal' and 'problem' output files is in the
> `Noshake mask` section, where normally ...
>
> .. snip ..
> Noshake mask :fmn; matches 50 atoms
> Removing shake constraints from C5_ fmn 139 -- H17 fmn 139
> Removing shake constraints from C5_ fmn 139 -- H18 fmn 139
> .. snip ..
>
> i am instead seeing the following,
>
> .. snip ..
> Noshake mask :fmn; matches 50 atoms
> Removing shake constraints from ^@^@^@^@^@^@^@^@^@^@^@^@^@ --
> ^@^@^@^@^@^@^@^@^@^@^@^@^@
> Removing shake constraints from ^@^@^@^@^@^@^@^@^@^@^@^@^@ --
> ^@^@^@^@^@^@^@^@^@^@^@^@^@
> .. snip ...

This is a bug in sander, in that it only creates residue-type names for
the first "matom" atoms (where matom is defined in nmr.h).

So, the simplest thing to do is to increase matom in nmr.h to a number larger
than the highest number of atom that a shake constraint will be removed.

Or:

apply the following patch to set.f:

*** set.f 3 Apr 2006 23:35:55 -0000 9.0
--- set.f 30 May 2007 21:36:43 -0000
***************
*** 665,670 ****
--- 665,671 ----
        jano = ix(ijbh+i-1)/3 + 1
        if( noshakegp( iano ) == 1 .or. noshakegp( jano ) == 1 ) then
           ix(noshake+i-1) = 1
+ if( iano<=matom .and. jano<=matom) &
           write(6,'(a,a,a,a)') ' Removing shake constraints from ', &
                resat(iano)(1:13),' -- ',resat(jano)(1:13)
           num_noshake = num_noshake + 1

>
> a DV/DL 'Averages' section is written every 1000 steps but all values in this
> section are zero for this latter simulation.

This sounds like a different problem, for which we would need more information
to be of any help.

....good luck....dac 

-- 

==================================================================
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.         |  skype:                 dacase
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
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