On Thu, Nov 24, 2011 at 12:47 AM, Jason Swails <jason.swails.gmail.com> wrote:
>> I run into another issue with a Na+ ion because the ff10 leaprc file
>> includes ions08.lib but doesn't fully parametrize the ions defined
>> there. Very confusing -- because ions are correctly recognized but the
>> topology can then anyway not be saved. A water-model-specific mod
>> file needs to be loaded to finish the job. I see that this is supposed
>> to be feature rather than bug but then it would be much less
>> troublesome to either have a complete parametrization (by default for
>> TIP3) or have no ion definitions included at all.
>>
>
> Different water models are appropriate for different simulations, so
> there's no water model we can just "assume" people will want. If we did,
> then we would mask errors for users that want to use, for example, TIP4P or
> TIP4Pew or something like that.
That's true. So a "default" may indeed be dangerous.
> Perhaps we could have a separate leaprc for different water models, so we'd
> have something like "source leaprc.ff10; source leaprc.tip3p" which would
> load the parameters and libraries for the water models as well as the ion
> parameters, I'm not sure which would be easier.
I think that would be a much better solution. Then ions would simply
be missing after the ff10 source command and people would pretty
quickly figure out that they need to source an additional leaprc for
that. What I found confusing is that ions are now kind of "half" there
which leads to errors that are not very informative, at least for more
casual users. Also it would be good if one wouldn't need to mess
around with mod files for a standard protein or DNA simulation with
ions. Previously, that used to be only necessary if there where really
non-standard residues in the system. Well, it's just a suggestion to
reduce the mail traffic on the Amber reflector :)
Thanks for your help.
Raik
>
> Furthermore, there's nothing stopping users from creating their own leaprc
> file if that's behavior that they want ;).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
--
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Raik Grünberg
http://www.raiks.de/contact.html
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Received on Thu Nov 24 2011 - 08:00:06 PST
