On Fri, Jan 25, 2013 at 8:08 AM, Vlad Cojocaru <
vlad.cojocaru.mpi-muenster.mpg.de> wrote:
> Hi all,
>
> I believe we found the problem ...
> Here it is:
>
> In the "ions94.lib" file (from the AMBER distribution) that we were
> loading for the ions, the "K+" leap unit is assigned a "K" type ...
> Therefore every time a "K+" is added in Leap it is directly assigned to
> a type "K" ..
>
> Our frcmod was actually modifying the "K+" type ...
>
> If I modify the "ions94.lib" and replaced the "K" with "K+" everywhere,
> the K+ is now properly overwritten from the frcmod.
>
> This is a very easy-to-make mistake so I hope this will help other
> people when they try to update K+ parameters via frcmod files.
>
> Maybe the developers could consider clearing up the different libraries
> so that such mistakes are avoided ....
>
This has already been done in the 'later' force fields---look at
ions08.lib. Is there a reason you are using ions94.lib?
I can't imagine we will ever change ions94.lib, since these kinds of silent
changes are often cruel to users expecting the 'original' behavior. The
appropriate solution is, IMO, to release a _new_ ion library with the
updated types and parameters and encourage people to use those.
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 25 2013 - 06:00:05 PST
