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 Tue Jan 12 2021 - 09:30:02 PST
