minimization can't always correct very bad initial structures. you should
look at the structure and try to determine the problem. It may be that you
need to make some adjustments (using a program like Chimera) before
minimization. This is really an issue with how you generated the initial
structure.
for the checkstructure error, are you sure the mdcrd file is not empty?
On Tue, Jan 12, 2021 at 12:20 PM MYRIAN TORRES RICO <
myriam.torres.iiq.csic.es> wrote:
> Ok, I have launched checkstructure in the min step and indeed I get a
> couple of residues very close to each other, my problem is that even
> minimizing it, this problem is not corrected...
>
> Another question, when I use checkstructure in the pressure step, it
> does not recognize my file.mdcrd and I get the following error
>
> Reading 'smp-193-ptn3rig.top' as Amber Topology
> Radius Set: H (N) -modified Bondi radii (mbondi2)
> INPUT: Reading input from 'coordprobe.in'
> [parm smp-193-ptn3rig.top]
> Warning: Topology 'smp-193-ptn3rig.top' already present.
> Warning: To load the same topology file multiple times use tags,
> Warning: e.g. `parm <file> [tag]`.
> [trajin smp-193ptn_pcon_tar.mdcrd]
> Reading 'smp-193ptn_pcon_tar.mdcrd' as Amber NetCDF
> Error: Netcdf file is empty.
> Error: Could not set up 'smp-193ptn_pcon_tar.mdcrd' for reading.
> Error: Could not set up input trajectory 'smp-193ptn_pcon_tar.mdcrd'.
> 1 errors encountered reading input.
> TIME: Total execution time: 0.1422 seconds.
> Error: Error (s) occurred during execution.
>
> I need to change the format, right?
>
>
> Thanks in advance,
>
> Myriam
>
>
>
> Carlos Simmerling <carlos.simmerling.gmail.com> escribió:
>
> > 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 Wed Jan 13 2021 - 05:00:02 PST
