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.
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Nov 16 2018 - 07:30:02 PST
