Dear Dan,
Thank you very much for your help!
Best regards,
Elvira.
сб, 17 нояб. 2018 г. в 00:11, Daniel Roe <daniel.r.roe.gmail.com>:
> Hi,
>
> I'm pretty sure the warnings are innocuous. Essentially for 1D runs,
> sander/pmemd will write replica/coordinate indices but not dimension
> info (like they do for multi-D runs). So when cpptraj encounters these
> trajectories it has to guess, and it defaults to temperature. However,
> this is currently a cosmetic warning and has no impact on processing
> the trajectories. If you see evidence that things are not working well
> let me know.
>
> TL;DR These warnings can be ignored, things are working.
>
> -Dan
> On Thu, Nov 15, 2018 at 11:22 PM Elvira Tarasova
> <elviratarasovachem.gmail.com> wrote:
> >
> > Dear Dan,
> >
> > Thank you for your response!
> > Cpptraj works in Amber18, and it gives me the next output:
> >
> >
> > "
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *Reading 'exp.modO.parm7' as Amber Topology Radius Set:
> > H(N)-modified Bondi radii (mbondi2)INPUT: Reading input from 'traj.in
> > <http://traj.in>' [trajin exp_remd_pH2_5_00001.nc.000 remdtraj
> > remdtrajtemp 5.0 trajnames
> >
> exp_remd_pH3_0_00001.nc.001,exp_remd_pH3_5_00001.nc.002,exp_remd_pH4_0_00001.nc.003,exp_remd_pH4_5_00001.nc.004,exp_remd_pH5_0_00001.nc.005,exp_remd_pH5_5_00001.nc.006,exp_remd_pH6_0_00001.nc.007]
> > Reading 'exp_remd_pH2_5_00001.nc.000' as Amber NetCDFWarning: New
> > style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
> > Assuming temperature.Warning: New style (Amber >= V18) remd values
> > detected with < 2 dimensions.Warning: Assuming temperature.Warning: New
> > style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
> > Assuming temperature.Warning: New style (Amber >= V18) remd values
> > detected with < 2 dimensions.Warning: Assuming temperature.Warning: New
> > style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
> > Assuming temperature.Warning: New style (Amber >= V18) remd values
> > detected with < 2 dimensions.Warning: Assuming temperature.Warning: New
> > style (Amber >= V18) remd values detected with < 2 dimensions.Warning:
> > Assuming temperature.Warning: New style (Amber >= V18) remd values
> > detected with < 2 dimensions.Warning: Assuming temperature. [trajout
> > REMD_only_5pH_00001.nc] Writing 'REMD_only_5pH_00001.nc' as Amber
> > NetCDF---------- RUN BEGIN
> > -------------------------------------------------PARAMETER FILES (1
> > total): 0: exp.modO.parm7, 129761 atoms, 42410 res, box: Orthogonal,
> 42185
> > mol, 41941 solventINPUT TRAJECTORIES (1 total): 0: REMD trajectories (8
> > total), lowest replica 'exp_remd_pH2_5_00001.nc.000' (reading 5000 of
> > 5000) Looking for frames at 5.00 K Coordinate processing will
> occur
> > on 5000 frames.*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *OUTPUT TRAJECTORIES (1 total): 'REMD_only_5pH_00001.nc' (5000 frames)
> is
> > a NetCDF AMBER trajectoryBEGIN TRAJECTORY
> > PROCESSING:....................................................ACTIVE
> > OUTPUT TRAJECTORIES (1): REMD_only_5pH_00001.nc (coordinates,
> temperature,
> > time, replica indices, coordinate indices, box)-----
> > exp_remd_pH2_5_00001.nc.000 (1-5000, 1) ----- 0% 10% 20% 30% 40% 50% 60%
> > 70% 80% 90% 100% Complete.Read 5000 frames and processed 5000
> frames.TIME:
> > Avg. throughput= 40.0985 frames / second.ACTION OUTPUT:TIME: Analyses
> took
> > 0.0000 seconds."*
> >
> >
> >
> > And everything looks fine, except lines
> > *"Warning: New style (Amber >= V18) remd values detected with < 2
> > dimensions.*
> > *Warning: Assuming temperature" *
> > I would like to ask, if the warnings are normal for the pH-REMD?
> >
> >
> > Best regards,
> > Elvira.
> >
> >
> > чт, 15 нояб. 2018 г. в 22:15, Daniel Roe <daniel.r.roe.gmail.com>:
> >
> > > Hi,
> > >
> > > The pH-REMD trajectory format changed in Amber 18, and cpptraj needed
> > > to change in order to process it. So you need to use cpptraj from
> > > Amber18 to process these trajectories. Let me know if you have trouble
> > > with Amber 18 cpptraj doing this.
> > >
> > > -Dan
> > >
> > > On Wed, Nov 14, 2018 at 11:26 PM Elvira Tarasova
> > > <elviratarasovachem.gmail.com> wrote:
> > > >
> > > > Dear Amber users,
> > > >
> > > > I am using the pH-REMD simulation with Amber, but I have some
> problems
> > > > connected with reconstruction of pH-based trajectory files.
> > > >
> > > > *When I perform cpptraj command:*
> > > > cpptraj exp.modO.parm7 traj.in
> > > >
> > > > *where traj.in <http://traj.in> file is:*
> > > > trajin exp_remd_pH2_5_00001.nc.000 remdtraj remdtrajtemp 5.0
> > > > exp_remd_pH3_0_00001.nc.001, exp_remd_pH3_5_00001.nc.002,
> > > > exp_remd_pH4_0_00001.nc.003, exp_remd_pH4_5_00001.nc.004,
> > > > exp_remd_pH5_0_00001.nc.005, exp_remd_pH5_5_00001.nc.006,
> > > > exp_remd_pH6_0_00001.nc.007
> > > > trajout REMD_only_5pH_00001.nc
> > > >
> > > > *I recieve the next error:*
> > > >
> > > > "Reading 'exp.modO.parm7' as Amber Topology
> > > > Radius Set: H(N)-modified Bondi radii (mbondi2)
> > > > INPUT: Reading input from 'traj.in'
> > > > [trajin exp_remd_pH2_5_00001.nc.000 remdtraj remdtrajtemp 5.0
> > > > exp_remd_pH3_0_00001.nc.001,exp_remd_pH3_5_00001.nc.002,
> > > > exp_remd_pH4_0_00001.nc.003, exp_remd_pH4_5_00001.nc.004,
> > > > exp_remd_pH5_0_00001.nc.005, exp_remd_pH5_5_00001.nc.006,
> > > > exp_remd_pH6_0_00001.nc.007]
> > > > Found 1 replicas.
> > > > Reading 'exp_remd_pH2_5_00001.nc.000' as Amber NetCDF
> > > > Error: Some or all replicas are missing temperature info.
> > > > Error: Could not set up input trajectory
> 'exp_remd_pH2_5_00001.nc.000'.
> > > > 1 errors encountered reading input.
> > > > TIME: Total execution time: 0.5414 seconds.
> > > > Error: Error(s) occurred during execution. "
> > > >
> > > >
> > > > Execution of the run is performed with pmemd.cuda.MPI, I use AMBER18
> for
> > > > the pH-REMD running and AMBER16 for cpptraj.
> > > >
> > > > I hope you can help me.
> > > >
> > > > Thank you in advance!
> > > > Best regards,
> > > > Elvira.
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Received on Sat Nov 17 2018 - 05:30:02 PST
