go all the way back to the first step after building the structure, and the
first energy output in that file. what does it say? is it a minimization
step?
you can use cpptraj to check for close contacts in your input coordinates,
this was discussed very recently here and you can find the emails in the
archive on ambermd.org
this post may be useful as well
http://archive.ambermd.org/201906/0336.html
On Tue, Jan 12, 2021 at 10:11 AM MYRIAN TORRES RICO <
myriam.torres.iiq.csic.es> wrote:
> Ok, I have checked the previous steps (minimization and heating) and
> in both, all the bond energies fluctuate a lot and indeed that of VDW
> is so high that it appears with (*).
> Knowing this ... how do I fix it? because the input comes from a
> previous docking and in the LEAP it didn't give me any problems...
>
> Thanks so much in advance,
>
>
> Myriam
>
>
> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>
> > your initial structure looks to have extremely high VDW energies. You
> > should check the end of the heating step that generated the coordinates
> > used as input here, and see if the energy was ok or not. If it was ok
> there
> > but not here, something must be different about the 2 runs.
> >
> > On Tue, Jan 12, 2021 at 9:38 AM MYRIAN TORRES RICO <
> > myriam.torres.iiq.csic.es> wrote:
> >
> >> Hi,
> >>
> >> I have launched again my script with nstlim=10 and ntpr=1 but I
> >> haven't find differences...(I have attached the new output).
> >>
> >> Thanks in advance
> >>
> >>
> >> myriam
> >> David A Case <david.case.rutgers.edu> escribió:
> >>
> >> > On Tue, Jan 12, 2021, MYRIAN TORRES RICO wrote:
> >> >>
> >> >> I have attached the output file where the error appears, in case it
> >> >> was helpful. If you need others files, tell me.
> >> >
> >> > Try setting nstlim=10 and ntpr=1. That might give you some
> information.
> >> >
> >> > ....dac
> >> >
> >> >
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Received on Tue Jan 12 2021 - 08:00:03 PST
