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.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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Received on Sun Jun 03 2007 - 06:07:15 PDT
