Dear Jason,
thanks for all the information. Made me a little bit smarter:) So I checked
the mdread.f (I think that’s the code you mean which is -wow- pretty
impressive:) ). So maybe a stupid questition but how do I get the parameters
for bromine?
I'm also doing some of my calculation with gbsa=1 again to compare the
difference to gbsa=2. In my opinion the difference is acceptable small so
they are still comparable but my boss is just a little bit squeamish so if
someone could give me a hint how to get those parameters that would be
fantastic :)
Thanks
Bernhard
-----Ursprüngliche Nachricht-----
Von: Jason Swails [mailto:jason.swails.gmail.com]
Gesendet: Mittwoch, 6. April 2011 23:31
An: AMBER Mailing List
Betreff: Re: [AMBER] bad atom type
Hello,
gbsa=1 uses LCPO to calculate the surface area (and the gradients wrt to the
surface areas), whereas gbsa=2 uses a different algorithm (it starts from an
icosahedron and recursively calculates spheres around atoms; it's described
more thoroughly in the manual and even more thoroughly in the code ;) ).
While they give similar answers, the only way to know for sure whether the
calculations need to be redone is to, in my opinion, redo the calculations
to check.
Luckily, though, GBSA calculations are fairly cheap, and re-running
calculations should be trivial if you've kept input files.
One more comment: the reason that gbsa=2 gave you that error and gbsa=1
didn't is because the LCPO parameters (p1, p2, p3, and p4) are assumed to be
the same as for a typical Carbon atom if the proper atom type is not found.
The only way to fix this approximation (if it's not good enough for you) is
to actually calculate the parameters that *should* be used for Br and add
them to the code.
Hope this helps,
Jason
On Tue, Apr 5, 2011 at 7:56 AM, Bernhard Poll
<poll.chemie.uni-hamburg.de>wrote:
> Hi Amber users,
>
>
>
> I calculated free energies using MMPBSA.py using a complex including
> bromine. So I got the following error
>
>
>
> Bad atom type: br
>
>
>
> Refering to an older mailing list entry I used the make-mdins flag and
> changed the gbsa from gbsa=2 to gbsa=1 an started the
>
> calculation again which worked fine then. I already calculated the
energies
> of some other ligands docked to the same protein using gbsa=2 and want to
> compare
>
> those. So my questition is if they are still comparable or how big is the
> difference between those options gbsa=1 and gbsa=2?If they are not is
there
> a faster option to
>
> get away from this bad atom type error or do I have to calculate the other
> complexes with gbsa=1 again?
>
>
>
> Thanks in advance
>
>
>
> Bernhard Poll
>
>
>
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Apr 07 2011 - 02:00:02 PDT
