On Wed, Mar 02, 2016, Prayagraj Fandilolu wrote:
>
>
> As you've said, I took a careful look into the leap outputs and tried to
> correct them with my original system.
>
> Today i tried loading two systems successively in two sessions.
>
> The warnings about improper torsion (old.log) were treated by adding an
> additional improper into the prepin file (new.log).
I think what Carlos (and others reading this) want is simpler example: do
you have a case (preferably with a *short* oligonucleotide) where you get
non-planar nitrogens, and that involves only standard nucleotides and no
additional changes or parameter files? We would need the leap.in file
that you used. (A good test case might involve just a single base.)
The point is to find out if there is really a bug in ff14SB, or whether
the problems you report are arising from changes you are making, either
with modified nucleotides or with making changes to a prepin file.
[Please note: on successive runs, tleap keeps adding to the end of the
leap.log file, so that you can get a file that contains information
about many separate tleap invocations. Please delete (or rename) your
"leap.log" file before running a test case. I find it almost impossible
to understand the files you sent for this reason, or even to locate what
you describe as "warnings about improper torsions". And the leap.in file is
generally more useful than the leap.log file, since the former makes it easier
to see what is being done, and to try to reproduce the problem.]
[Second note: if you can make a small test case, then the "printDihedrals"
command in parmed can be used to examine the torsion parameters in a given
prmtop file without having you be overwhelmed with output. Or, even in a
bigger system, use "printDihedrals <mask>" can be used to focus attention on a
single base.]
...thanks...dac
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Received on Wed Mar 02 2016 - 05:00:03 PST
