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

From: Ben Sattelle <ben.sattelle.postgrad.manchester.ac.uk>
Date: Wed, 30 May 2007 23:05:20 +0100

i will apply the patch, many thanks for this, Ben.

> 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 - 06:07:16 PDT
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