Yes Jason, you are right ... Thanks
I somehow unconsciously related this library with Tom's parameters ...
So when we decided to use Smith/Dang parameters, we chose to load
ions94.lib ..
But yes, of course, the library can be used with any set of parameters ...
Vlad
On 01/25/2013 02:53 PM, Jason Swails wrote:
> 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
>
--
Dr. Vlad Cojocaru
Max Planck Institute for Molecular Biomedicine
Department of Cell and Developmental Biology
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]mpi-muenster.mpg.de
http://www.mpi-muenster.mpg.de/research/teams/groups/rgcojocaru
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Received on Fri Jan 25 2013 - 06:30:03 PST
