AMBER Archive (2002)

Subject: Re: bug in New2oldparm

From: David A. Case (case_at_scripps.edu)
Date: Thu Sep 19 2002 - 10:28:30 CDT

On Thu, Sep 19, 2002, Pascal Bonnet wrote:
>
>
> I think there is a bug in the program new2oldparm.
>
> topology file created by AMBER7 and then converted by New2oldparm
> title
> 163 8 78 92 177 135 391 347 0 0 962 8
> 92 135 347 9 17 18 8 0 0 0 0 0
> 0 0 0 0 21 0 0
>
> topology file created by AMBER6 (correct format 12i6)
> title
> 163 8 78 92 177 135 391 347 0 0 962 8
> 92 135 347 9 17 18 8 0 0 0 0 0
> 0 0 0 0 21 0
>

Thanks for the report. I think the best fix is to update carnal to ignore the
final number (if it is present). Basically, sander in amber 7 requires the
the 31st parameter to be there (although it is often 0). If the "old" file
was only going to be used for amber 6, one could just not write it out in the
new2oldparm program. But, some people will surely plan to use the "old"
format in amber 7 as well, so that value needs to be there.

Of course, this means that the "old" format created by new2oldparm is in fact
slightly different than the files created by amber6 LEaP :-( If anybody
has good suggestions, I'd welcome them.

I'll look into updating carnal to do the right thing.

..thanks...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.         |  home page:                   
La Jolla CA 92037  USA            |    http://www.scripps.edu/case
==================================================================