This one might be worth tracking down: looks like "solvateBox" is somehow
changing its behavior(?) I could see that being a problem if people were
trying to reproduce old workflows. How big is the difference in numbers of
waters?
I spent some time looking at it and it was an error on my part that led to
something interesting. For that test I forgot to add the line source
leaprc.water.tip3p to the leap.in file. Adding that line results in the
test passing.
Without the HW/OW parameters, leap writes a pdb file with water coordinates
and the number of waters differs by 13. In the leap.log it has a note "type
- hence mass - of one or more atoms could not be found)" and " (using
default radius 1.500000 for O)". I am assuming that most likely the
difference in the number of waters is influenced by the change in the
radius?
The test does not write a solvated parm7 file. I added a line to write a
solvated parm7 and it fails as expected because there are no HW and OW
parameters. I am not sure if we want to allow pdb files being written with
the default oxygen radius but since generating the parm7 file will fail
without the parameters then it may be okay?
I can start making the changes and submit it in the meantime.
On Tue, Mar 9, 2021 at 12:06 PM David A Case <david.case.rutgers.edu> wrote:
> On Tue, Mar 09, 2021, Kellon Belfon wrote:
> >
> >Therefore I started my test by removing all mentions of HW and OW
> >parameters from these parmxx.dat files. By doing this approach users will
> >have to explicitly source the tip3p leaprc (leaprc.water.tip3p) in order
> to
> >get the HW and OW parameters for tip3p.
>
> Kellon: this is great!
>
> >
> > - If anyone else does not object (big possibility I am missing some
> > knowledge on how things were done in amber in the past) then I propose
> to
> > regenerate the topology and leap log files for the test failures with
> > NTYPES and NPHB differences.
> >
> > - I also proposed to change the leap.in for the tests that fail to
> > source leaprc.water.tip3p.
>
> I'm in favor of both of these, but might also be missing something...
>
> >One of the test case $AMBERHOME/AmberTools/test/leap/Run.cmds tend to
> give
> >different water coordinates and number of water molecules when source
> >leaprc.water.tip3p vs keeping the tip3p parameters in the parm10.dat file
>
> This one might be worth tracking down: looks like "solvateBox" is somehow
> changing its behavior(?) I could see that being a problem if people were
> trying to reproduce old workflows. How big is the difference in numbers of
> waters?
>
> ...thanks...dac
>
>
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>
--
Kellon A. A. Belfon, Graduate Student
Carlos Simmerling Laboratory
The Laufer Center for Physical and Quantitative Biology
The Department of Chemistry, Stony Brook University
Stony Brook, New York 11794
Phone: (347) 546-4237 <(347)+546+4237> Email: kellon.belfon.stonybrook.
<kellon.belfon.stonybrook.edu>edu
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Received on Tue Mar 09 2021 - 11:00:02 PST
